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Resource Description Total Records Last Updated
ArrayExpress ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compli ... [more]ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED recommendations. The ArrayExpress Data Warehouse stores gene-indexed expression profiles from a curated subset of experiments in the repository. [less] 35,877 2013-02-05
Adverse Event Reporting System Data Adverse Event Reporting System (AERS) Databases are validated and normalized to provide consist ... [more]Adverse Event Reporting System (AERS) Databases are validated and normalized to provide consistent results to our users that depend on data such as this for research into Adverse Events reported to the FDA by Consumers, Doctors and many other health care related professionals. [less] 1,172,881 2012-03-06
AgingGenesDB (via NIF) This database provides a searchable and browsable list of aging related genes and their effects ... [more]This database provides a searchable and browsable list of aging related genes and their effects on longevity. Other information can also be found including: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. The Biology of Aging at the University of Washington is the home of the Nathan Shock Center of Excellence in the Basic Biology of Aging and the Genetic Approaches to Aging Training Grant. The University of Washington is a major center for research in Gerontology, and these programs help to enrich the infrastructure for this work. [less] 346 2012-09-04
AutDB (via NIF) AutDB is a public database of data from scientific publications for autism spectrum disorders. ... [more]AutDB is a public database of data from scientific publications for autism spectrum disorders. It also includes several interactive modules that highlight the genes implicated in autism: Human Gene, Animal Models, and Protein Interactions. [less] 268 2012-10-11
BioModels BioModels Database is a repository of peer-reviewed, published, computational models. These mat ... [more]BioModels Database is a repository of peer-reviewed, published, computational models. These mathematical models are primarily from the field of systems biology, but more generally are those of biological interest. This resource allows biologists to store, search and retrieve published mathematical models. In addition, models in the database can be used to generate sub-models, can be simulated online, and can be converted between different representational formats. This resource also features programmatic access via Web Services. [less] 863 2012-11-27
Biositemaps Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly ... [more]Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. [less] 2,434 2012-03-06
caNanoLab caNanoLab is a data sharing portal designed to facilitate information sharing in the biomedical ... [more]caNanoLab is a data sharing portal designed to facilitate information sharing in the biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. [less] 895 2012-03-08
caArray caArray is an open-source, web and programmatically accessible array data management system. ca ... [more]caArray is an open-source, web and programmatically accessible array data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG™). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management. [less] 182 2012-06-08
Cell Centered Database (via NIF) The Cell Centered Database is a publicly accessible resource for high resolution 2D, 3D and 4D ... [more]The Cell Centered Database is a publicly accessible resource for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB. The goal of the CCDB project is to make unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Data in the CCDB can be accessed by performing a Search or by browsing through our Gallery. Data in the CCDB may be downloaded freely and reused for non-profit use within the terms of our usage agreement. [less] 431 2012-06-26
Conserved Domain Database (CDD) The Conserved Domain Database (CDD) contains protein domain models imported from outside source ... [more]The Conserved Domain Database (CDD) contains protein domain models imported from outside sources, such as Pfam and SMART, and curated at NCBI. CDD contains over 12,000 such models and is linked to other NCBI databases, including protein sequences, bibliographic citations, and taxonomy. [less] 46,346 2012-03-09
ClinicalTrials.gov ClinicalTrials.gov provides regularly updated information about federally and privately support ... [more]ClinicalTrials.gov provides regularly updated information about federally and privately supported clinical research in human volunteers. ClinicalTrials.gov gives you information about a trial's purpose, who may participate, locations, and phone numbers for more details. The information provided on ClinicalTrials.gov should be used in conjunction with advice from health care professionals. Before searching, you may want to learn more about clinical trials. [less] 122,591 2012-03-08
DrugBank DrugBank is offered to the public as a freely available resource. Use and re-distribution of th ... [more]DrugBank is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (DrugBank) and the original publication. [less] 4,774 2012-03-12
Drug Related Gene Database (via NIF) The Related Gene (DRG) Database gene expression data are extracted from published journal artic ... [more]The Related Gene (DRG) Database gene expression data are extracted from published journal articles that test hypotheses relevant to the neuroscience of addiction and addictive behavior. Data types include the effects of a particular drug, strain, or knock out on a particular gene, in a particular anatomical region. [less] 47,840 2013-01-20
Database of Genotypes and Phenotypes The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the re ... [more]The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. Such studies include genome-wide association studies, medical sequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits. [less] 269 2012-02-05
GEMMA (via NIF) Gemma is a database and software system for the meta-analysis of gene expression data. Gemma co ... [more]Gemma is a database and software system for the meta-analysis of gene expression data. Gemma contains data from hundreds of public microarray data sets, referencing hundreds of published papers. Users can search, access and visualize coexpression and differential expression results. [less] 634 2013-01-07
GeneNetwork (via NIF) The GeneNetwork consists of a set of linked resources for systems genetics. It has been designe ... [more]The GeneNetwork consists of a set of linked resources for systems genetics. It has been designed for multiscale integration of networks of genes, transcripts, and traits such as toxicity, cancer susceptibility, and behavior. This open resource combines more than 25 years of legacy data generated by hundreds of scientists with full genome sequence and deep transcriptome data sets. WebQTL is the leading GeneNetwork module, and has been optimized for on-line analysis of traits that are controlled by combinations of allelic variants and environmental factors. WebQTL exploits several permanent genetic reference populations (GRP) of mouse (BXD, LXS, etc.), rat (HXB), and Arabidopsis (BayXSha). Each GRP is accompanied by dense genetic maps used to locate modifiers that cause downstream differences in expression and higher-order phenotypes, including disease susceptibility. [less] 386,156 2012-10-10
Gene Expression Omnibus DataSets A gene expression/molecular abundance repository supporting MIAME compliant data submissions, ... [more]A gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval. [less] 31,483 2012-03-09
ARRS GoldMiner ARRS GoldMiner provides instant access to images published in selected peer-reviewed radiology ... [more]ARRS GoldMiner provides instant access to images published in selected peer-reviewed radiology journals. This new, web-based system allows viewers to search for images by findings, anatomy, imaging technique, and patient age and sex. [less] 1,155 2012-03-06
Integrated Disease View (via NIF) The NIF Integrated Disease View is a virtual database currently indexing authoritative informat ... [more]The NIF Integrated Disease View is a virtual database currently indexing authoritative information on disease and treatment options from NINDS Disorder List - http://www.ninds.nih.gov/disorders/disorder_index.htm and PubMed Health - http://www.ncbi.nlm.nih.gov/pubmedhealth [less] 2,104 2013-01-20
ModelDB (via NIF) ModelDB provides an accessible location for storing and efficiently retrieving computational ne ... [more]ModelDB provides an accessible location for storing and efficiently retrieving computational neuroscience models. ModelDB is tightly coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. ModelDB is a curated database of published models in the broad domain of computational neuroscience. It addresses the need for access to such models in order to evaluate their validity and extend their use. It can handle computational models expressed in any textual form, including procedural or declarative languages (e.g. C , XML dialects) and source code written for any simulation environment. The model source code doesn't even have to reside inside ModelDB; it just has to be available from some publicly accessible online repository or WWW site. ModelDB is curated in order to maximize the scientific utility of its contents. The ideal model entry would contain "original" (author-written) source code, especially if it works and reproduces at least one figure from a published article. Original source code has tremendous value because it is what the authors used to generate the simulation results from which they derived their published insights and conclusions. High quality "third party" re-implementations of published models are also relevant, especially those involving models that are of wide interest. [less] 707 2012-05-04
MICAD Molecular Imaging and Contrast Agent Database 823 2012-03-06
Integrated Videos (via NIF) The NIF Integrated Video View is a virtual database currently indexing video and other multimed ... [more]The NIF Integrated Video View is a virtual database currently indexing video and other multimedia content from NIH VideoCasting and Podcasting, JoVE: Journal of Visualized Experiments, The Guardian: Science Videos and Biointeractive. JoVE is a peer reviewed, PubMed indexed journal devoted to the publication of biological research in a video format and NIH video is a vast archive of scientific talks given at various NIH meetings and functions. [less] 8,980 2012-12-02
Online Mendelian Inheritance in Man OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenot ... [more]OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. [less] 22,186 2012-03-09
Pathway Commons Pathway Commons is a convenient point of access to biological pathway information collected fro ... [more]Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. [less] 2,323 2012-03-13
PubChem PubChem provides information on the biological activities of small molecules. It is a component ... [more]PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. [less] 121,349 2012-03-09
PDSP Ki database (via NIF) The PDSP Ki database is a unique resource in the public domain which provides information on th ... [more]The PDSP Ki database is a unique resource in the public domain which provides information on the abilities of drugs to interact with an expanding number of molecular targets. The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes. The query interface is designed to let you search by any field, or combination of them to refine your search criteria. The flexible user interface also provides for customized data mining. [less] 47,304 2012-06-26
PharmGKB [Disease] PharmGKB curates information that establishes knowledge about the relationships among drugs, di ... [more]PharmGKB curates information that establishes knowledge about the relationships among drugs, diseases and genes, including their variations and gene products. [less] 837 2012-03-05
PharmGKB [Drug] PharmGKB curates information that establishes knowledge about the relationships among drugs, di ... [more]PharmGKB curates information that establishes knowledge about the relationships among drugs, diseases and genes, including their variations and gene products. [less] 1,643 2012-03-05
PharmGKB [Gene] PharmGKB curates information that establishes knowledge about the relationships among drugs, di ... [more]PharmGKB curates information that establishes knowledge about the relationships among drugs, diseases and genes, including their variations and gene products. [less] 1,242 2012-01-24
PubMed PubMed is a service of the U.S. National Library of Medicine that includes over 17 million cit ... [more]PubMed is a service of the U.S. National Library of Medicine that includes over 17 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources. [less] 1,158,025 2011-10-24
PubMedHealth Drugs (via NIF) PubMed Health is a consumer health Web site produced by the National Center for Biotechnology I ... [more]PubMed Health is a consumer health Web site produced by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at the National Institutes of Health (NIH). PubMed Health provides up-to-date information on diseases, conditions, injuries, drugs, supplements, treatment options, and healthy living, with a special focus on comparative effectiveness research from institutions around the world. [less] 1,158 2012-10-22
PubMedHealth Tests (via NIF) PubMed Health, a consumer health Web site, provides up-to-date information on diseases, conditi ... [more]PubMed Health, a consumer health Web site, provides up-to-date information on diseases, conditions, injuries, drugs, supplements, treatment options, and healthy living, with a special focus on comparative effectiveness research from institutions around the world. PubMed Health includes consumer guides summarizing comparative effectiveness research, fact sheets on diseases and conditions, information on drugs and supplements, encyclopedic overviews of health topics, links to external Web sites. PubMed Health has a special focus on comparative effectiveness research, in particular that research which evaluates the available evidence of the benefits and harms of different treatment options for different groups of people. In Comparative Effectiveness Research, experts often synthesize the evidence from dozens, or even hundreds, of individual studies. [less] 832 2012-12-13
Reactome A curated knowledgebase of biological pathways. 208,093 2012-03-08
NIH RePORTER (via NIF) The RePORTER resource has replaced the CRISP database. RePORT is a searchable database of feder ... [more]The RePORTER resource has replaced the CRISP database. RePORT is a searchable database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions. The Research Portfolio Online Reporting Tools (RePORT) Website provides a central point of access to reports, data, and analyses of NIH research. [less] 102,443 2013-02-07
ResearchCrossroads Centralizing scientific and medical funding data so that researchers gain recognition for their ... [more]Centralizing scientific and medical funding data so that researchers gain recognition for their work and funders make better investments. [less] 1,033,651 2012-03-06
Stanford Microarray Database The Stanford Microarray Database (SMD) serves as a microarray research database for Stanford in ... [more]The Stanford Microarray Database (SMD) serves as a microarray research database for Stanford investigators and their collaborators. [less] 18,838 2012-03-12
ToxinDB (via NIF) Toxin and Toxin Target Database (T3DB) is a unique bioinformatics resource that combines detail ... [more]Toxin and Toxin Target Database (T3DB) is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. The database currently houses over 2900 toxins described by over 34200 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to over 1300 corresponding toxin target records. Altogether there are over 33800 toxins, toxin target associations. Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5600 sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches. [less] 2,946 2012-06-22
UniProt KB The mission of UniProt is to provide the scientific community with a comprehensive, high-qualit ... [more]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. [less] 533,515 2012-02-27
WikiPathways WikiPathways was established to facilitate the contribution and maintenance of pathway informat ... [more]WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. [less] 1,721 2012-03-09