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on page 1 showing 20 out of 49 results from 1 sources

    Addgene

Cite this (Addgene, RRID:SCR_002037)

URL: http://www.addgene.org

Resource Type: Resource, catalog, data or information resource, database

A non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. They work with laboratories to assemble a high-quality library of published and useful plasmids and their associated cloning/sequence data for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request. There is no cost to deposit plasmids to Addgene and it will store samples in triplicate (including one at an offsite backup facility), sequence key regions for validation, and handle the appropriate Material Transfer Agreements (MTAs) with institutions. Additionally, users can create a webpage that directs scientists to request plasmids. Material Transfer Agreements (MTAs) allow open exchange to occur because they offer intellectual property and liability protection for material providers. Institutions that have deposited materials at Addgene require a MTA for each transfer of material.

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Cite this (Animal Imaging Database, RRID:SCR_008002)

URL: http://aidb.crbs.ucsd.edu

Resource Type: Resource, database, service resource, storage service resource, image repository, data repository, data or information resource

THIS RESOURCE IS NO LONGER AVAILABLE. Documented October 4, 2017.

A sub-project of the Cell Centered Database (http://ccdb.ucsd.edu) providing a public repository for animal imaging data sets from MRI and related techniques. The public AIDB website provides the ability for browsing, visualizing and downloading the animal subjected MRI data. The AIDB is a pilot project to serve the current need for public imaging repositories for animal imaging data. The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy. The AIDB data model is modified from the basic model of the CCDB where microscopic images are combined to make 2D, 3D and 4D reconstructions. The CCDB has made available over 40 segmented datasets from high resolution magnetic resonance imaging of inbred mouse strains through the prototype AIDB. These data were acquired as part of the Mouse BIRN project by Drs. G. Allan Johnson and Robert Williams. More information about these data can be found in Badea et al. (2009) (Genetic dissection of the mouse CNS using magnetic resonance microscopy - Pubmed: 19542887)

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Cite this (Antibody Registry, RRID:SCR_006397)

URL: http://antibodyregistry.org/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Public registry of antibodies with unique identifiers for commercial and non-commercial antibody reagents to give researchers a way to universally identify antibodies used in publications. The registry contains antibody product information organized according to genes, species, reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones). Data is provided in many formats so that authors of biological papers, text mining tools and funding agencies can quickly and accurately identify the antibody reagents they and their colleagues used. The Antibody Registry allows any user to submit a new antibody or set of antibodies to the registry via a web form, or via a spreadsheet upload.

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    AutDB

Cite this (AutDB, RRID:SCR_001872)

URL: http://autism.mindspec.org/autdb/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Curated public database for autism research built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The genetic information includes data from linkage and association studies, cytogenetic abnormalities, and specific mutations associated with ASD. New gene submissions are welcome. Modules: * Human Gene: thoroughly annotated list of genes that have been studied in the context of autism, with information on the genes themselves, relevant references from the literature, and the nature of the evidence. Uniquely, SFARI Gene incorporates information on both common and rare variants. * Animal Model: information about lines of genetically modified mice that represent potential models of autism. This information includes the nature of the targeting construct, the background strain and, most importantly, a thorough summary of the phenotypic features of the mice that are most relevant to autism. * Protein Interaction (PIN): compilation of all known direct protein interactions for those gene products implicated in autism. It presents both graphical and tabular views of interactomes, highlighting connections between autism candidate genes. Each protein interaction is manually verified by consultation with the primary reference. * Copy Number Variant (CNV): a parallel resource providing genetic information about all known copy number variants linked to autism. * Gene Scoring: includes a "score" for each autism candidate gene, based on an assessment of the strength of human genetic evidence.

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Cite this (Avian Brain Circuitry Database, RRID:SCR_002401)

URL: http://www.behav.org/abcd/abcd.php

Resource Type: Resource, image collection, spatially referenced dataset, service resource, storage service resource, atlas, image repository, data repository, data or information resource

THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017.

Database developed for storing, retrieving and cross-referencing neuroscience information about the connectivity of the avian brain. It contains entries about the new and old terminology of the areas and their hierarchy and data on connections between brain regions, as well as a functional keyword system linked to brain regions and connections.

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Cite this (BAMS Connectivity, RRID:SCR_000561)

URL: http://brancusi.usc.edu/

Resource Type: Resource, data or information resource, database

Database of information about brain region circuitry, it collates data from the literature on tract tracing studies and provides tools for analysis and visualization of connectivity between brain regions.

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Cite this ( Beta Cell Biology Consortium , RRID:SCR_005136)

URL: http://www.betacell.org/

Resource Type: Resource, organization portal, resource, organism supplier, antibody supplier, database, biomaterial supply resource, biospecimen repository, experimental protocol, consortium, narrative resource, material resource, service resource, portal, storage service resource, cell repository, reagent supplier, data repository, material storage repository, data or information resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 1, 2015. Consortium that aims to facilitate interdisciplinary collaborations to advance the understanding of pancreatic islet development and function, with the goal of developing innovative therapies to correct the loss of beta cell mass in diabetes, including cell reprogramming, regeneration and replacement. They are responsible for collaboratively generating the necessary reagents, mouse strains, antibodies, assays, protocols, technologies and validation assays that are beyond the scope of any single research effort. The scientific goals for the BCBC are to: * Use cues from pancreatic development to directly differentiate pancreatic beta cells and islets from stem / progenitor cells for use in cell-replacement therapies for diabetes, * Determine how to stimulate beta cell regeneration in the adult pancreas as a basis for improving beta cell mass in diabetic patients, * Determine how to reprogram progenitor / adult cells into pancreatic beta-cells both in-vitro and in-vivo as a mean for developing cell-replacement therapies for diabetes, and * Investigate the progression of human type-1 diabetes using patient-derived cells and tissues transplanted in humanized mouse models. Many of the BCBC investigator-initiated projects involve reagent-generating activities that will benefit the larger scientific community. The combination of programs and activities should accelerate the pace of major new discoveries and progress within the field of beta cell biology.

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Cite this (bioDBcore, RRID:SCR_002781)

URL: http://biodbcore.org

Resource Type: Resource, narrative resource, database, standard specification, data or information resource

A community-defined, uniform, generic description of the core attributes of biological databases. The BioDBCore checklist is overseen by the International Society for Biocuration (ISB), in collaboration with the BioSharing forum. A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them have been partly compiled with the support of Oxford University Press and Re3Data.org. Database providers are encouraged to either create or claim their BioDBCore entry and update it as appropriate.

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    BioGRID

Cite this (BioGRID, RRID:SCR_007393)

URL: http://www.thebiogrid.org/

Resource Type: Resource, database, service resource, storage service resource, software resource, data repository, data or information resource

A curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. The current version searches over 41,000 publications containing over 720,000 interactions (June 2014) and contributions are welcome. Complete coverage of the entire literature is maintained for budding yeast (S. cerevisiae), fission yeast (S. pombe) and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. It provides interaction data to several model organism databases, resources such as Entrez-Gene, SGD, TAIR, FlyBase and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including IMEx compatible PSI MI XML. For developers, BioGRID interactions are also available via a REST based Web Service and Cytoscape plugin.

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Cite this (BioNumbers, RRID:SCR_002782)

URL: http://bionumbers.hms.harvard.edu/

Resource Type: Resource, data or information resource, database

Database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. Along with the numbers, you'll find the relevant references to the original literature, useful comments, and related numbers. While always of importance to biologists, having numbers in hand is becoming increasingly critical for experimenting, modeling, and analyzing biological systems. BioNumbers was motivated by an appreciation of how long it can take to find even the simplest number in the vast biological literature. All numbers are taken directly from a literature source and that reference is provided with the number. BioNumbers is designed to be highly searchable and queries can be performed by keywords or browsed by menus. BioNumbers is a collaborative community platform where registered users can add content and make comments on existing data. All new entries and commentary are curated to maintain high quality.

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Cite this (Brain Architecture Management System, RRID:SCR_007251)

URL: http://brancusi.usc.edu/bkms/

Resource Type: Resource, data repository, ontology, database, service resource, storage service resource, controlled vocabulary, data or information resource

Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. BAMS is also an online knowledge management system designed to handle neurobiological information at different levels of organization of the vertebrate nervous system (NS).

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Cite this (Brede Database, RRID:SCR_003327)

URL: http://hendrix.imm.dtu.dk/services/jerne/brede/

Resource Type: Resource, data or information resource, database

A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments.

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Cite this (Cell Centered Database, RRID:SCR_002168)

URL: http://ccdb.ucsd.edu

Resource Type: Resource, database, service resource, storage service resource, image repository, data repository, data or information resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. 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 microscope 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.

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Cite this (CellML Model Repository, RRID:SCR_008113)

URL: http://www.cellml.org/models

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.

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    CHEBI

Cite this (CHEBI, RRID:SCR_002088)

URL: http://www.ebi.ac.uk/chebi/

Resource Type: Resource, data or information resource, database

A database of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. ChEBI uses nomenclature, symbolism and terminology endorsed by the International Union of Pure and Applied Chemistry (IUPAC) and the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). Molecules directly encoded by the genome (e.g. nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI.

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Cite this (CIL - Cell Image Library, RRID:SCR_003510)

URL: http://www.cellimagelibrary.org/

Resource Type: Resource, database, service resource, storage service resource, image repository, data repository, data or information resource

Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.

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Cite this (Comparative Toxicogenomics Database, RRID:SCR_006530)

URL: http://ctdbase.org/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks.

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Cite this (Coriell Cell Repositories, RRID:SCR_003244)

URL: https://catalog.coriell.org/

Resource Type: Resource, production service resource, biomaterial supply resource, biospecimen repository, database, material service resource, service resource, storage service resource, cell repository, data or information resource, material resource, biomaterial manufacture, material storage repository

A biorepository and biomaterial supply resource which establishes, verifies, maintains, and distributes cells, cultures and DNA derived from cell cultures to the scientific community around the world. Scientists can browse the sample catalog and request specific cell lines for their research studies. An inventory of the remaining stock of each cell line and DNA preparation is presented in real time. Coriell's significant cell biobank collections include: NIGMS Human Genetic Cell Repository, NINDS Human Genetics DNA and Cell Line Repository, NIA Aging Cell Repository, NHGRI Sample Repository for Human Genetic Research, NEI Age-Related Eye Disease Study (AREDS) Genetic Repository, HD Community BioRepository, American Diabetes Association, GENNID Study, and Autism Research Resource. The repositories are ISO 9000-2001 compliant.

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    CRCNS

Cite this (CRCNS, RRID:SCR_005608)

URL: http://crcns.org

Resource Type: Resource, database, collaborative tool, catalog, service resource, storage service resource, data repository, data or information resource

Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS also offers funding for a new class of proposals focused on the sharing of data and other resources.

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    DrugBank

Cite this (DrugBank, RRID:SCR_002700)

URL: http://www.drugbank.ca/

Resource Type: Resource, data or information resource, database

Bioinformatics and cheminformatics database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database includes FDA-approved small molecule drugs, FDA-approved biotech (protein and peptide) drugs, nutraceuticals and experimental drugs. Additionally, non-redundant protein (i.e. drug target, enzyme, transporter, and carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug and chemical data and the other half devoted to drug target or protein data. Users may query DrugBank in any number of ways.

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