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Showing 1 to 13 of 13 open-source 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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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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DrugBank: Open Data Drug & Drug Target Database

Provider: David Wishart/University of Alberta, CA
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Descriptions: A bio- and chemical informatics resource that combines detailed drug (chemical, pharmacological and pharmaceutical) data with comprehensive drug targeting (sequence, structure, and pathway) information. The database contains nearly 4300 drug entries, including FDA-approved small molecule drugs, FDA-approved biotech (protein/peptide) drugs, "nutraceuticals" and experimental drugs. Contains more than 6,800 drug entries with almost 4,300 non-redundant protein sequences linked. Each entry, or  DrugCard, contains more than 80 data fields, half of which are devoted to drug/chemical data and the other half to drug target/protein data. Downloads and information on rights, acknowledgement and usage are available here.
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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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Gold Book (IUPAC Compendium of Chemical Terminology)

Provider: IUPAC (International Union of Pure and Applied Chemistry)
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Descriptions: One of a series of Colour Books for chemical nomenclature, terminology, symbols and units. Search the Compendium by text or structure, use an alphabetical index, ring index, math/physics terms index, and more. Interactive graphics (link maps) show how term entries are interrelated and allow navigation through a complex web of connections. References to the literature are included, and are also links. "In the most recent version, the Gold Book is accompanied by a suite of software tools that enable the users to simply add links to the Gold Book to their online materials, especially HTML. These tools are based on tools that are used internally in production of the Gold Book. The software tools are placed separately onSourceForge which allows for easier collaboration on the software."
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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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NCMIR – National Center for Microscopy and Imaging Research

Provider: National Center for Microscopy and Imaging Research/University of California San Diego
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Descriptions: NCMIR develops technologies to facilitate understanding of biological systems from the gross anatomical to the molecular scale and makes those technologies available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes can be easily obtained and analyzed.
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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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Neuroscience Information Framework

Provider: National Institutes of Health
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Descriptions: The Neuroscience Information Framework is a dynamic inventory of web-based neuroscience resources: data, materials, and tools. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment. The NIF project is designed to serve the biomedical research community. The more participation from the community, the better the NIF... Collaborating institutions working on the current version of NIF include University of California, San Diego, California Institute of Technology, George Mason University, Yale University Medical College, and Washington University.
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NIH Data Sharing Repositories

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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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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STAR (Software Tools for Academics and Researchers)

Provider: MIT (Massachusetts Institute of Technology)
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Descriptions: The STAR program team designs software exploring core scientific research concepts, innovative and intuitive teaching tools for classroom use, helping to close the gap between scientific research and the classroom. So far, STAR units include: STARBiochem, a protein visualization tool (structural biology); STARBiogene, a set of genomic visual and analytic tools; STARGenetics (analysis of genetic traits); STARHydro (hydrology visualization); STARMolSim (molecular dynamics simulations); and STARHPC (parallel programming education.)
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