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Showing 1 to 11 of 11 items tagged as data-sharing


Protein Data Bank: An Information Portal to Biological Macromolecular Structures

database

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

database

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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Effective Health Care Program – AHRQ

database

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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NIH Data Sharing Repositories

database

Provider: National Institutes of Health/National Library of Medicine
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Descriptions: This is a portal with a sortable list of 45 NIH and outside entities' data repositories and data-sharing facilitation sites that offer open-source software. Links to submission and download policies and instructions are provided for each. Research areas include: genomics of the nematode, drosophila, zebrafish and rat; sequencing data; peptides and proteins; pathogens and vectors; the NCI cancer imaging repository; neuroscience, rare diseases, Parkinson's, autism, and more.
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Better Data, Better Health

website

Provider: Robert Wood Johnson Foundation
Descriptions: This website contains data sets, reports and rankings that include information on the quality of care delivery, patient outcomes, and patient feedback on physicians, hospitals, and cost. A "data hub" provides interactive graphics of state populations broken out by ethnicity, educational attainment, and age group for a number of healthcare measures, such as rates of the uninsured, portion of state budgets spent on healthcare, healthcare quality, and more. The focus of this website is discussion and demonstration of how "big data" can serve to improve health care in the United States.
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NeuroMorpho.org

database

Provider: George Mason University
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Descriptions: NeuroMorpho.Org is the largest collection to date of publicly-accessible 3-D neuronal reconstructions and associated metadata in a curated repository. It contains a Neuron Atlas (a spatial distribution visualization tool.) Neurons from more than 20 species are represented. Browse by species, brain region, cell type or source; search by keyword, metadata or morphometry. The What’s new page has information on newly-released data, including new species strains, brain regions, cell types, and experimental conditions. The Acknowledgements include details on contributing labs, and the About page provides an updated overview of the repository content. OntoSearch enables more powerful searches of species and strains with automated synonym translation, taxonomical relations, and keyword auto-completion. The literature coverage database includes publications through March 2014.
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NDB: Nucleic Acid Database

database

Provider: The Nucleic Acids Database Research Project/Rutgers University
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Descriptions: A portal for 3-D structural information about nucleic acids, the NDB contains information about experimentally-determined nucleic acids and complex assemblies. Search by annotations relating to sequence, structure and function; download, analyze, and learn about nucleic acids.
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NCBI (National Center for Biotechnology Information)

database

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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Mendeley

database

Provider: Mendeley Ltd.
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Descriptions: Mendeley is an open-access reference management tool. Use drag-and-drop to add references to your list, or add via web import. Easily create bibliographies and insert citations into papers by adding a plug-in for your word processing program. Includes an integral pdf viewer that allows highlighting and annotation. Organize with list-sorting and by adding folders. Mendeley also provides for creation of one's own research profile and for setting up private and public groups for collaboration and sharing, with additional useful features for keeping everything clear and organized. A crowd-sourced catalog of citations provided in public groups can be viewed by subject area and individual citations may be downloaded to one's account. A subscription version of Mendeley provides expanded storage for groups and individuals, and technical support, space and flexible collaboration features for "Team" implementations.
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Neuroscience Information Framework 3.1

website

Provider: National Institutes of Health
Descriptions: The Neuroscience Information Framework (NIF) is a semantically-enhanced portal to a dynamic inventory of Web-based neuroscience resources. An initiative of the NIH Blueprint for Neuroscience Research, NIF enhances discovery and access to often unindexed but publicly available research data, datasets, software and tools in the deep web, as well as linking to PubMed records and open-access literature. The NIF Project provides the NIF Registry, Antibody Registry, Drug Related Gene Database, neuroscience ontology and a way to contribute to it (via the NeuroLex wiki) and semantic tagging services. NIF Navigator, a customizable, stand-alone search tool for incorporation into websites or wikis, draws query results from all the NIF's own components and from other sites and accessible databases. The valuable resources at NIF are too numerous to be described adequately here.
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ALFRED: The Allele Frequency Database

database

Provider: Kenneth K. Kidd, Yale University / US National Science Foundation
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Access Level:
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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