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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)

Physical Resource or Software Tool Software

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
PfamResource, data or information resource, databaseA database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).database, clan, structure, sequence, protein family, domainSCR_004726(Pfam, RRID:SCR_004726)Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EMBL core funds, Howard Hughes Medical Institute, Wellcome Trustrelated to: Conserved Domain Database, Monarch Initiative, SUPFAM, DBD: Transcription factor prediction database, DOMINE: Database of Protein Interactions, GeneSpeed- A Database of Unigene Domain Organization , Eukaryotic Linear Motif, TopoSNP, GOTaxExplorer, TrED, ProOpDB, Algal Functional Annotation Tool, used by: Mutation Annotation and Genomic Interpretation, MobiDB, listed by: OMICtoolsReferences (2)Last checked downnlx_72111, OMICS_01696http://pfam.sanger.ac.uk/
ChEMBLResource, data or information resource, databaseCollection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database.database, compound, data, bioassay, bioactive, molecule, drug, discoverySCR_014042(ChEMBL, RRID:SCR_014042)EMBL Member States, EU Innovative Medicines Initiative, GSK, Medicines for Malaria Ventures, Pfizer, Syngenta, Wellcome Trustused by: GEROprotectors, PubChemPMID:21948594Last checked up
FlyMineResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceAn integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java APIanopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publicationSCR_002694(FlyMine, RRID:SCR_002694)University of Cambridge; Cambridge; United Kingdom NHGRI, Wellcome Trustrelated to: FlyBase, Universal Protein Resource, Ensembl, InterPro, BioGRID, Research Collaboratory for Structural Bioinformatics Protein Data Bank, Tree families database, IntAct, Gene Ontology, GOA, ArrayExpress, REDfly Regulatory Element Database for Drosophilia, KEGG, ReactomePMID:17615057Last checked upnif-0000-02845
Wellcome-CTC Mouse Strain SNP Genotype SetResource, data set, data or information resourceData set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34.genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strainSCR_003216(Wellcome-CTC Mouse Strain SNP Genotype Set, RRID:SCR_003216)Wellcome Trust Centre for Human Genetics NCRR, NIAAA, NIGMS, NIMH, NINDS, Wellcome TrustLast checked upnlx_156947
PRIDEResource, service resource, data or information resource, data repository, storage service resource, databaseCentralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomartSCR_003411(PRIDE, RRID:SCR_003411)European Bioinformatics Institute BBSRC, European Union FP7, Wellcome Trustrelated to: HUPO Proteomics Standards Initiative, ProteomeXchange, used by: ProteomeXchange, BioSample Database at EBI, listed by: Biositemaps, re3data.orgReferences (2)Last checked upnif-0000-03336
European Nucleotide ArchiveResource, service resource, data or information resource, data repository, storage service resource, databasePublic archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.analysis, bioinformatics, dna, nucleotide, sequencing, web service, rna, molecular biology, nucleotide sequence, protein, gene expression, gene, genome, biochemistry, molecular structure, metabolite, protein binding, chemogenomics, gold standardSCR_006515(European Nucleotide Archive, RRID:SCR_006515)European Bioinformatics Institute EMBL, European Union, Wellcome Trustrelated to: NCBI Sequence Read Archive, ENA Sequence Version Archive, VBASE2, DDBJ Sequence Read Archive, ISA Infrastructure for Managing Experimental Metadata, DDBJ - DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan, NCBI, INSDC, INSDC, NCBI Assembly Archive Viewer, used by: BioSample Database at EBI, listed by: 3DVC, re3data.org, OMICtoolsPMID:20972220Last checked upnif-0000-32981, OMICS_01029http://www.ebi.ac.uk/embl/
PomBaseResource, service resource, data or information resource, data repository, storage service resource, databaseModel organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation, mailing lists, and welcomes data submissions.fission yeast, gene ontology, genome sequence, schizosaccharomyces pombe (4896), schizosaccharomyces pombe, dna, protein, cosmic assembly, intron, go, chromosome, telomere, centromere, mating region, data mapping, model organism, genomeSCR_006586(PomBase, RRID:SCR_006586)University of Cambridge; Cambridge; United Kingdom , European Bioinformatics Institute , University College London; London; United Kingdom Wellcome Trustrelated to: AmiGO, GeneDB Spombe, used by: NIF Data Federation, listed by: 3DVCPMID:22039153Last checked upnlx_144356http://www.sanger.ac.uk/Projects/S_pombe/
NeuronVisioResource, d visualization softwareA Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections'''' properties and it offers easy integration with matplotlib for plotting the results. The geometry can be saved using NeuroML and the computational results in a customized and extensible HDF5 format; the results can then be reload in the software and analyzed in a later stage, without re-running the simulation. Featuring 3D visualization of the model with the possibility to change it runtime; creation of vectors to record any variables present in the section; pylab integration to plot directly the result of the simulation; exploration of the timecourse of any variable among time using a color coded scale; saving the results simulation for later analysis; automatic download and running of models in ModelDB.3d visualization, electrophysiological model, hdf storage, matplotlib integration, neuron model, visualization, neuron, visualization, electrophysiologySCR_006839(NeuronVisio, RRID:SCR_006839)European Bioinformatics Institute Wellcome Trustrelated to: INCF Software Center, NEURON, ModelDBPMID:22685429Last checked upnlx_156723
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