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on page 1 showing 20 out of 30 results from 1 sources

    BIND

Cite this (BIND, RRID:SCR_003576)

URL: http://bind.ca/

Resource Type: Resource, data or information resource, database

Peer-reviewed biomolecular database containing over 200,000 published interactions and complexes for more than 60,000 unique gene identifiers. The growing data in BINDplus contain over 1,500 unique organisms, and 7,555 Gene Ontology terms derived from peer-reviewed scientific data extracted from over 23,800 journal articles and over 9000 corresponding authors.

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Cite this (BioCarta Pathways, RRID:SCR_006917)

URL: http://www.biocarta.com/

Resource Type: Resource, data or information resource, database

BioCarta Pathways allows users to observe how genes interact in dynamic graphical models. Online maps available within this resource depict molecular relationships from areas of active research. In an open source approach, this community-fed forum constantly integrates emerging proteomic information from the scientific community. It also catalogs and summarizes important resources providing information for over 120,000 genes from multiple species. Find both classical pathways as well as current suggestions for new pathways.

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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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    CORUM

Cite this (CORUM, RRID:SCR_002254)

URL: http://mips.helmholtz-muenchen.de/genre/proj/corum

Resource Type: Resource, data or information resource, database

Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded.
The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%).

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Cite this (Database of Interacting Proteins, RRID:SCR_003167)

URL: http://dip.doe-mbi.ucla.edu/

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

Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available.

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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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Cite this (HPRD - Human Protein Reference Database, RRID:SCR_007027)

URL: http://www.hprd.org

Resource Type: Resource, data or information resource, database

Database that represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.

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Cite this (HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism, RRID:SCR_007050)

URL: http://humancyc.org/

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

The HumanCyc database describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional analysis of Homo sapiens at the genomic level. A computational pathway analysis of the human genome assigned human enzymes to predicted metabolic pathways. Pathway assignments place genes in their larger biological context, and are a necessary step toward quantitative modeling of metabolism. HumanCyc contains the complete genome sequence of Homo sapiens, as presented in Build 31. Data on the human genome from Ensembl, LocusLink and GenBank were carefully merged to create a minimally redundant human gene set to serve as an input to SRI''s PathoLogic software, which generated the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome''s annotation. SRI did not re-annotate the genome, but worked with the gene function assignments in Ensembl, LocusLink, and GenBank. The resulting pathway/genome database (PGDB) includes information on 28,783 genes, their products and the metabolic reactions and pathways they catalyze. Also included are many links to other databases and publications. The Pathway Tools software/database bundle includes HumanCyc and the Pathway Tools software suite and is available under license. This form of HumanCyc is faster and more powerful than the Web version.

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    InnateDB

Cite this (InnateDB, RRID:SCR_006714)

URL: http://www.innatedb.com

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

Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice.

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    IntAct

Cite this (IntAct, RRID:SCR_006944)

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

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

Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.

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Cite this (Integrating Network Objects with Hierarchies, RRID:SCR_002084)

URL: http://www.inoh.org

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

INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form. The system provides pathway information as a composite of biological events, since functional knowledge is usually described as a set of fragmented processes. Each event is annotated with entries of a event ontology, which also has links to GO.

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    KEGG

Cite this (KEGG, RRID:SCR_012773)

URL: http://www.kegg.jp/

Resource Type: Resource, topical portal, data access protocol, database, web service, production service resource, data analysis service, analysis service resource, service resource, portal, software resource, data or information resource

An integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in the completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism, and the ecosystem. Analysis tools are also available. KEGG may be used as a reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.

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    MatrixDB

Cite this (MatrixDB, RRID:SCR_001727)

URL: http://matrixdb.univ-lyon1.fr/

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

Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions.

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    MINT

Cite this (MINT, RRID:SCR_001523)

URL: http://mint.bio.uniroma2.it/

Resource Type: Resource, data or information resource, database

A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.

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Cite this (MIPS Mammalian Protein-Protein Interaction Database, RRID:SCR_008207)

URL: http://mips.gsf.de/proj/ppi/

Resource Type: Resource, data or information resource, database

The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators. It is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions. To suit different users needs we provide a variety of interfaces to search the database: -Expert interface Simple but powerful boolean query language. -PPI search form Easy to use PPI search -Protein search Just find proteins of interest in the database Sponsors: This work is funded by a grant from the German Federal Ministry of Education and Research.

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    NetPath

Cite this (NetPath, RRID:SCR_003567)

URL: http://www.netpath.org/

Resource Type: Resource, data or information resource, database

A manually curated resource of signal transduction pathways in humans. All pathways are freely available for download in BioPAX level 3.0, PSI-MI version 2.5 and SBML version 2.1 formats. The slim pathway models representing only core reactions in each pathway are available at NetSlim. All the NetPath pathway models are also submitted to WikiPathways.

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Cite this (Pathway Interaction Database, RRID:SCR_006866)

URL: http://pid.nci.nih.gov

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 27, 2016. Curated database of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. All interactions are assembled into pathways, and can be accessed by performing searches for biomolecules, or processes, or by viewing predefined pathways. This was a collaborative project between the NCI and Nature Publishing Group (NPG) from 2006 until September 22nd, 2012, and is no longer being updated. PID is aimed at the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. The database focuses on the biomolecular interactions that are known or believed to take place in human cells. It can be browsed as an online encyclopedia, used to run computational analyses, or employed in ways that combine these two approaches. In addition to PID''''s predefined pathways, search results are displayed as dynamically constructed interaction networks. These features of PID render it a useful tool for both biologists and bioinformaticians. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is supplemented by a concise editorial section that includes specially written synopses of recent important research articles in areas related to cancer research, and specially commissioned Bioinformatics Primers that provide practical advice on how to make the most of other relevant online resources. The database and editorial content are updated monthly, and users can opt to receive a monthly email alert to stay informed about new content. Note: as of September 23, 2012 the PID is no longer being actively curated. NCI will maintain the PID website and data for twelve months beyond September 2012 to allow interested parties to obtain the previously curated data before the site is retired in September 2013.

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    PDB

Cite this (PDB, RRID:SCR_012820)

URL: http://www.rcsb.org/pdb/

Resource Type: Resource, data or information resource, database

A worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. It contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. The RCSB PDB curates and annotates PDB data according to agreed upon standards. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome. Users can perform simple or complex queries on the data and analyze and visualize the results. FTP and Web services are also available. RCSB PDB staff are located at Rutgers, the State University of New Jersey and the University of California, San Diego.

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    PDZBase

Cite this (PDZBase, RRID:SCR_003568)

URL: http://abc.med.cornell.edu/pdzbase

Resource Type: Resource, data or information resource, database

A manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. It currently contains 339 experimentally determined protein protein interactions.

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    PharmGKB

Cite this (PharmGKB, RRID:SCR_002689)

URL: http://www.pharmgkb.org/

Resource Type: Resource, data access protocol, database, web service, data set, service resource, storage service resource, software resource, data repository, data or information resource

Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.

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