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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
MINTResource, data or information resource, databaseA 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.protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, orthologSCR_001523(MINT, RRID:SCR_001523)University of Rome Tor Vergata; Rome; Italy AIRC Associazione Italiana per la Ricerca sul Cancro, ENFIN, European Union, HUPO Proteomics Standards Initiative, IMEx - The International Molecular Exchange Consortium, Interaction Proteome Projectrelated to: MPIDB, TissueNet - The Database of Human Tissue Protein-Protein Interactions, InteroPorc, Interaction Reference Index, Pathway Commons, ConsensusPathDB, VirusMINT, PSICQUIC Registry, Agile Protein Interactomes DataServer, uses: IntAct, PSI-MI, listed by: re3data.org, affiliated with: IMEx - The International Molecular Exchange Consortium, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (8)Last checked upnlx_152821
MatrixDBResource, service resource, data or information resource, production service resource, databaseFreely 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.extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interactionSCR_001727(MatrixDB, RRID:SCR_001727)Claude Bernard University Lyon 1; Lyon; France European Unionrelated to: IMEx - The International Molecular Exchange Consortium, Gene Ontology, PSI-MI, HPRD - Human Protein Reference Database, Interaction Reference Index, ConsensusPathDB, IMEx - The International Molecular Exchange Consortium, PSICQUIC Registry, IntAct, listed by: re3data.orgReferences (2)Last checked upnif-0000-10226http://matrixdb.ibcp.fr/
InteroPorcResource, source code, data analysis service, data analysis software, data processing software, database, analysis service resource, software application, production service resource, service resource, software resource, data or information resourceAutomatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, proteinSCR_002067(InteroPorc, RRID:SCR_002067)CEA; Gif sur Yvette; France European Union, French Atomic Energy Commission, French National Agency of Research, Marie Curie Fellowshiprelated to: Integr8 : Access to complete genomes and proteomes, IntAct, MINT, Database of Interacting Proteins, PSICQUIC RegistryPMID:18508856Last checked upnif-0000-20816
InnateDBResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourcePublicly 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.gene, immune response, pathway, protein, signaling pathway, interaction, immune, signaling response, gene, orthology prediction, orthology, ortholg, annotation, interactome, gene expression, molecule, protein-protein interaction, molecular interaction, visualization, nucleic acid-protein, nucleic acid, network, web service, transcription factor binding site, software resourceSCR_006714(InnateDB, RRID:SCR_006714)Simon Fraser University; British Columbia; Canada , University of British Columbia; British Columbia; Canada Microbial infection, Allergy, AsthmaAllerGen, European Union, Michael Smith Foundation for Health Research, Teagascrelated to: IMEx - The International Molecular Exchange Consortium, Interaction Reference Index, ConsensusPathDB, IMEx - The International Molecular Exchange Consortium, PSICQUIC Registry, PSICQUIC, Gene Ontology, IntAct, listed by: re3data.org, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (2)Last checked upnif-0000-20808
IntActResource, service resource, data or information resource, data repository, storage service resource, databaseOpen 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.protein domain, motif, protein interaction, molecular interaction, interaction, protein, binary interaction, complex, data set, protein-protein interaction, pathway, small molecule-protein, nucleic acid-protein, small molecule, nucleic acid, protein binding, chromatin, cancer, apoptosis, molecular biology, virus, source code, isoform, gold standardSCR_006944(IntAct, RRID:SCR_006944)European Bioinformatics Institute European Unionrelated to: 3D-Interologs, IMEx - The International Molecular Exchange Consortium, MPIDB, TissueNet - The Database of Human Tissue Protein-Protein Interactions, InteroPorc, Interaction Reference Index, Pathway Commons, ConsensusPathDB, FlyMine, IMEx - The International Molecular Exchange Consortium, Integrated Molecular Interaction Database, VirHostNet: Virus-Host Network, PSICQUIC Registry, Universal Protein Resource, SIB Swiss Institute of Bioinformatics, I2D, InnateDB, MatrixDB, MBInfo, AgBase, Cardiovascular Gene Ontology Annotation Initiative, PSI-MI, Monarch Initiative, Agile Protein Interactomes DataServer, used by: ChannelPedia, MINT, Pathway Analysis Tool for Integration and Knowledge Acquisition, listed by: 3DVC, re3data.org, OMICtools, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (5)Last checked upnif-0000-03026, OMICS_01918
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