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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
Swedish Twin RegistryResource, people resource, patient registryThe Swedish Registry was established in the 1960s to study how smoking affects our health. Then little was known about the dangers of smoking. There is, at present, information on approximately 85 000 twin pairs, both monozygotic and dizygotic. As described by Lichtenstein et al., 2002, Pedersen et al., 2002 and Lichtenstein et al., 2006, the Swedish Twin Registry (STR) is the largest and most comprehensive twin registry in the world. Founded in 1961, the registry covers all like-sexed twin births since 1886, and all twin births (like- and unlike-sexed) since 1906. There are currently 89,000 pairs of twins registered, of which both members of 65,000 pairs are alive, with regular updates concerning vital status, addresses, hospital discharges, tumors, and causes of death, through subscriptions to national registries. Furthermore, there is extensive epidemiological data (exposures, symptoms and disease through questionnaires or interviews) on all pairs born 1986 or earlier, for most individuals involving 30 year baseline to follow-up information. Furthermore, data from the cohort of twins born since 1991 have been or will be contacted with a telephone interview with the parents of twins as they turn 9 (CATSS). Because the STR is an (inter)national resource, we are receptive to collaboration academic and industry-based researchers. Regardless of the type of research all potential collaborations or data access agreements must be first reviewed Steering Committee of the STR.zygosity, age, sex, education, monozygotic, dizygotic, child, adolescent, adult, tobacco, nicotine, gene, environmentSCR_008883(Swedish Twin Registry, RRID:SCR_008883)Karolinska Institutet; Stockholm; Sweden Twin, Smoking, Agingrelated to: KI Biobank - Gallstone, KI Biobank - KOL, KI Biobank - KTS, KI Biobank STAGE-ADHD, KI Biobank - EuroClot, KI Biobank - Economical Behavior, CATSS - Child and Adolescent Twin Study in Sweden, DOGSS, KI Biobank - SALTY, KI Biobank - STAGE, KI Biobank - Parkinson, KI Biobank - HARMONY, Twin Study of Child and Adolescent Development - TCHAD, KI Biobank - TwinGene, used by: KI Biobank - STAR, KI Biobank - SATSALast checked downnlx_151292http://ki.se/ki/jsp/polopoly.jsp?d=9610&l=en
ZooBankResource, data or information resource, controlled vocabulary, databaseA database of scientific names in zoology. ZooBank is an online, open-access, community-generated registry for zoological nomenclature. It serves as a service to taxonomists, biologists, and the global diversity informatics community. It is the Official Register of the International Commission on Zoological Nomenclature (ICZN).zoo, bank, taxonomy, biology, global diversity, informatics, registry, zoology, iczn, official register of the international commission on zoological nomenclatureSCR_000901(ZooBank, RRID:SCR_000901)NSFLast checked upnlx_156872
SysZNF - C2H2 Zinc Finger genesResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. SysZNF is an information resource for C2H2 Zinc Finger genes in humans and mice. C2H2 Zinc Finger genes (C2H2-ZNF) constitute the largest class of transcription factors in humans and mouse. C2H2 zinc finger proteins primarily bind to DNA. In most cases, they attach to regions near certain genes and turn the genes on and off as needed. The researches on these genes show light on the evolution of gene regulation systems and development. Therefore, we develop SysZNF (Systematical information resource of Zinc Finger genes) to collect the information related to C2H2 Zinc Finger genes. The aim of SysZNF was to provide a user-friendly interface for rendering the information (DNA, Expression, Protein, Reference and so on) of each C2H2-ZNF (e.g., ZNF10) and to enable a comprehensive analysis of C2H2-ZNF. This project was supported by the Proteome-Center at Rostock University (PCRU) who conceives the concept of the database and Key laboratory of Systems biology at the Shanghai Institute for Biological Sciences (SIBS) who implemented the database. It is maintained jointly by PCRU and SIBS.zinc finger protein, zinc finger, cysteine, histidine, zinc ion, geneSCR_007056(SysZNF - C2H2 Zinc Finger genes, RRID:SCR_007056)University of Rostock; Mecklenburg-Vorpommern; Germany , Chinese Academy of Sciences; Beijing; China BMBF, Chinese Academy of SciencesPMID:18974185Last checked downnif-0000-03530
Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core Resource, service resource, resource, core facility, access service resourceZebrafish core facility which generates and maintains transgenic and mutant fish lines for hematology research. It also provides expertise and training in model production, study design, and fish production for research.zebrafish model, transgenic fish, mutant fish lineSCR_015355( Boston Children's Hospital Center of Excellence in Molecular Hematology Zebrafish Core , RRID:SCR_015355) Boston Children's Hospital Center of Excellence in Molecular Hematology NIDDKlisted by: NIDDK Information NetworkLast checked down
Zebrafish International Resource CenterResource, antibody supplier, material analysis service, analysis service resource, biomaterial supply resource, production service resource, service resource, storage service resource, biomaterial analysis service, reagent supplier, material storage repository, material resource, organism supplierCenter that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species.zebrafish line, expressed sequence tag, cdna, fish, antibody, pathology, research, embryo, adultSCR_005065(Zebrafish International Resource Center, RRID:SCR_005065)University of Oregon; Oregon; USA NCRR, NICHD, NIH Office of the Director, W.M. Keck Foundationrelated to: One Mind Biospecimen Bank Listing, ZMP, NIF Data Federation, Zebrafish Information Network, zfishbook, used by: Integrated Animals, listed by: One Mind Biospecimen Bank ListingLast checked upnif-0000-00242http://zebrafish.org/home/guide.php
Zebrafish Genome ProjectResource, data or information resource, databaseDatabase of zebrafish genome.Zebrafish, genomeSCR_013157(Zebrafish Genome Project, RRID:SCR_013157)Wellcome Trust Sanger Institute; Hinxton; United Kingdom related to: Genome Reference Consortium, Zebrafish Information NetworkLast checked upnif-0000-31931, SCR_017503https://www.sanger.ac.uk/science/data/zebrafish-genome-project
Zebrafish Neuroscience Research ConsortiumResource, group, training resourceA group of scientists who collaborate and promote zebrafish neuroscience research. The consortium has opportunities for networking, scholarly publications and zebrafish-related symposia and conferences. The consortium is a supporter of the Zebrafish Neurophenome Project (ZNP), an initiative for a database of zebrafish behavioral and physiological data in an online, open source format.zebrafish, consortium, research, publication, scholar, neuroscience, behavioral activitySCR_000298(Zebrafish Neuroscience Research Consortium, RRID:SCR_000298)Last checked upnlx_151974
Zebrafish Neurophenome Project DatabaseResource, data set, service resource, data repository, storage service resource, data or information resourceDatabase of neurobehavioral and physiological data of adult zebrafish models, complementing the available repositories for zebrafish genetic information, by providing a dynamic, open-access data repository of comprehensive, curated collection of results from zebrafish neurobehavioral experiments. As of May 2012, it contains over 4,500 experimental results, from over 75 unique physiological and behavioral tests and 330 different drug treatments. ZNP incorporates validated and curated data from work published in this field, to improve the accessibility of current knowledge to researchers interested in using adult zebrafish models. Overall, this program will allow investigators to rapidly review data, to direct their research using these models. Data and protocol submissions are now being accepted.zebrafish, behavior, pharmacology, psychopharmacology, drug, adult zebrafish, phenotype, model, neurobehavior, physiologySCR_004482(Zebrafish Neurophenome Project Database, RRID:SCR_004482) Zebrafish Neuroscience Research Consortium , Tulane University School of Medicine; Louisiana; USA NIDA, Tulane University; Louisiana; USAlisted by: 3DVCPMID:22171801Last checked upnlx_143762http://www.tulane.edu/%E2%88%BCznpindex/search
MaizeGDBResource, topical portal, database, analysis service resource, organism-related portal, data analysis service, service resource, portal, production service resource, storage service resource, data repository, data or information resourceCollection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images.zea mays, corn, model organism, genome, locus, metabolic pathway, genetics, genomics, sequence, gene product, function, literature reference, phenotype, trait, pest, gel pattern, mutant, blast, gene, image, corn, genotype-environment interaction, gene mapping, plant genome mapping, plant genome, gold standardSCR_006600(MaizeGDB, RRID:SCR_006600)University of Maryland; Maryland; USA National Corn Growers Association, NSF, USDA, USDA/ARSrelated to: GenBank, listed by: re3data.org, OMICtools, works_with: Maize Database of Images and GenomesReferences (4)Last checked upnif-0000-03096, OMICS_01655
University of Zaragoza; Zaragoza; SpainResource, undergraduate program resource, graduate program resource, degree granting program, training resourceAn undergraduate and postgraduate university which is located in Zaragoza, Spain.zaragoza, university, undergraduate, postgraduateSCR_000341(University of Zaragoza; Zaragoza; Spain, RRID:SCR_000341)Last checked upnlx_144537
Yunnan University; Yunnan; ChinaResource, undergraduate program resource, graduate program resource, degree granting program, training resourceAn university in China which offers undergraduate, master's, and doctorate degrees. This organization has a total of 20 different programs.yunnan, chinese university, doctoral degree, university, institutionSCR_000344(Yunnan University; Yunnan; China, RRID:SCR_000344)Last checked upnlx_157806
GSE4698Resource, data set, data or information resourceCurated data set where gene expression profiling was performed on 60 prospectively collected samples of children with first relapse of acute lymphoblastic leukemia enrolled on the relapse trial ALL-REZ BFM 2002 of the Berlin-Frankfurt-Muenster study group.young human, gene expression, relapse, male, female, gene expression profile, childSCR_003644(GSE4698, RRID:SCR_003644)RanchoBiosciences Cancer, Acute lymphoblastic leukemiarelated to: Gene Expression OmnibusLast checked downnlx_157795
NIH MRI Study of Normal Brain DevelopmentResource, data set, narrative resource, experimental protocol, data or information resourceData sets of clinical / behavioral and image data are available for download by qualified researchers from a seven year, multi-site, longitudinal study using magnetic resonance technologies to study brain maturation in healthy, typically-developing infants, children, and adolescents and to correlate brain development with cognitive and behavioral development. The information obtained in this study is expected to provide essential data for understanding the course of normal brain development as a basis for understanding atypical brain development associated with a variety of developmental, neurological, and neuropsychiatric disorders affecting children and adults. This study enrolled over 500 children, ranging from infancy to young adulthood. The goal was to study each participant at least three times over the course of the project at one of six Pediatric Centers across the United States. Brain MR and clinical/behavioral data have been compiled and analyzed at a Data Coordinating Center and Clinical Coordinating Center. Additionally, MR spectroscopy and DTI data are being analyzed. The study was organized around two objectives corresponding to two age ranges at the time of enrollment, each with its own protocols. * Objective 1 enrolled children ages 4 years, 6 months through 18 years (total N = 433). This sample was recruited across the six Pediatric Study Centers using community based sampling to reflect the demographics of the United States in terms of income, race, and ethnicity. The subjects were studied with both imaging and clinical/behavioral measures at two year intervals for three time points. * Objective 2 enrolled newborns, infants, toddlers, and preschoolers from birth through 4 years, 5 months, who were studied three or more times at two Pediatric Study Centers at intervals ranging from three months for the youngest subjects to one year as the children approach the Objective 1 age range. Both imaging and clinical/behavioral measures were collected at each time point. Participant recruitment used community based sampling that included hospital venues (e.g., maternity wards and nurseries, satellite physician offices, and well-child clinics), community organizations (e.g., day-care centers, schools, and churches), and siblings of children participating in other research at the Pediatric Study Centers. At timepoint 1, of those enrolled, 114 children had T1 scans that passed quality control checks. Staged data release plan: The first data release included structural MR images and clinical/behavioral data from the first assessments, Visit 1, for Objective 1. A second data release included structural MRI and clinical/behavioral data from the second visit for Objective 1. A third data release included structural MRI data for both Objective 1 and 2 and all time points, as well as preliminary spectroscopy data. A fourth data release added cortical thickness, gyrification and cortical surface data. Yet to be released are longitudinally registered anatomic MRI data and diffusion tensor data. A collaborative effort among the participating centers and NIH resulted in age-appropriate MR protocols and clinical/behavioral batteries of instruments. A summary of this protocol is available as a Protocol release document. Details of the project, such as study design, rationale, recruitment, instrument battery, MRI acquisition details, and quality controls can be found in the study protocol. Also available are the MRI procedure manual and Clinical/Behavioral procedure manuals for Objective 1 and Objective 2.young human, child, pediatric, experimental protocol, brain, brain development, development, mri, minc, clinical, behavior, anatomical mri, diffusion tensor imaging, mr spectroscopy, adolescent, clinical data, behavioral data, data visualization software, clinical measure, behavioral measure, physical neurological examination, behavioral rating, neuropsychological testing, structured psychiatric interview, hormonal measure, image collection, neonate, clinical neuroinformatics, dicom, minc2, magnetic resonance, niftiSCR_003394(NIH MRI Study of Normal Brain Development, RRID:SCR_003394)National Institutes of Health Healthy, NormalNICHD, NIDA, NIH Blueprint for Neuroscience Research, NIMH, NINDSrelated to: NIH Data Sharing Repositories, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC), Biositemaps, NIH Data Sharing RepositoriesLast checked downnif-0000-00201http://www.bic.mni.mcgill.ca/nihpd/info/, https://nihpd.crbs.ucsd.edu/nihpd/info/index.html
Treatment of SSRI-resistant Depression in Adolescents (TORDIA)Resource, disease-related portal, topical portal, research forum portal, portal, clinical trial, data or information resourceA multi-site, clinical research study examining treatment options for teens whose depression has not improved after one adequate trial of a selective serotonin reuptake inhibitor (SSRI), a type of antidepressant. The purpose of the study is to determine how best to treat adolescents with depression that is resistant to the first SSRI antidepressant they have tried. Participants receive one of three other antidepressant medications, either alone or in combination with cognitive behavioral therapy. The TORDIA study aims to develop useful clinical guidelines for the care and management of adolescent depression. Adolescents ages 12 to 18, currently taking a prescribed selective serotonin reuptake inhibitor (SSRI) and still experiencing depression, participate in a 12-week randomized treatment study that includes one of four conditions: (1) switching to an alternative SSRI, (2) switching to a different non-SSRI antidepressant, (3) switching to an alternative SSRI and receiving cognitive behavioral therapy (CBT), or (4) switching to a different non-SSRI antidepressant and receiving CBT. This is a double-blind study, which means that neither the participant nor the clinical staff will know which of the three possible medications has been assigned. Participants who respond to the assigned treatment will receive 12 additional weeks of the same treatment. Those who do not appear to be getting better will be offered 12 weeks of an alternative, individualized treatment plan based on each participant''s particular needs. All participants will receive follow-up psychiatric evaluations for 12 months after the 12-week continuation phase of the study, regardless of treatment adherence. For more information visit, http://www.clinicaltrials.gov/ct2/show/NCT00018902?term=clinical+trial+AND+treatment+of+ssri-resistant+AND+depression+AND+TORDIA+AND+study&rank=1young human, adolescent, depression, depressive disorder, clinical trial, selective serotonin reuptake inhibitor, antidepressant, nct00018902, drug, fluoxetine, venlafaxine, behavioral therapy, cognitive behavioral therapy, citalopram, treatmentSCR_008831(Treatment of SSRI-resistant Depression in Adolescents (TORDIA), RRID:SCR_008831)ClinicalTrials.gov Depressive Disorder, Resistant to the first SSRI antidepressantNIMHused by: Limited Access Datasets From NIMH Clinical TrialsPMID:20478877Last checked downnlx_146237
Phaff Yeast Culture CollectionResource, service resource, organization portal, data or information resource, portal, databaseCollection of wild yeast in the world. Academic and industrial resarchers utilize this collection for a variety of research and applications, including pigments, enzymes, food ingredients, and hosts for protein expression. Provides contract screening and strain selection services.yeast, strain, wild, screening, selection, serviceSCR_016781(Phaff Yeast Culture Collection, RRID:SCR_016781)University of California at Davis; California; USA submitted by: Resource Identification PortalLast checked up
Genome Resources for Yeast ChromosomesResource, data or information resource, databaseDatabase which provides annotated sequence data for the genomes of basidio and ascomycete yeasts. The resources provided include genetic element pages, data sets for downloading, quick and advanced searches, facilities for BLAST comparisons, and a genome browser powered by JBrowse from GMOD.yeast, single celled eukaryote, annotated genome, basidio yeast, ascomycete yeastSCR_015005(Genome Resources for Yeast Chromosomes, RRID:SCR_015005)uses: JBrowseLast checked up
YeastFuncResource, image, database, data or information resourceYeastFunc is a public database for browsing of quantitative S. cerevisiae gene function predictions, gene function linkage predictions, and the evidence behind the predictions, overlayed upon the experimentally verified annotations as taken from the SGD, MGI and Ensembl Gene databases, respectively. Three aspects of gene function predictions are displayed: * First, for a particular gene, users can view all functions ranked by certainty that the corresponding gene-function pair is a true annotation. * Second, for a particular function, users can view all genes ranked by certainty. * The third aspect is functional linkage predictions, displayed alongside the first two aspects as gene-centered and function-centered images, respectively, and editable via Cytoscape. These functional linkage graphs are independently informative, though they are also used as a step in one of the gene function prediction techniques whose certainty scores are displaying on this site, so they can be treated as evidence. Evidence leading to all gene function predictions in the first two aspects as well as all experimentally verified gene function annotation is displayed alongside each of the first two aspects, allowing the user to understand the basis for the certainty score. To get started type a Gene Ontology ID, an SGD ID, an ORF ID, an Ensembl gene id, an Entrez gene id, a Uniprot id, a standard gene name, or a general search term in the text box. The results of your search will appear below the search box. These results are solely Gene Ontology terms and genes for the species that you selected. Click the result that you would like to investigate further. Note the paging toolbar at the bottom of the results list. If you are interested in performing your own analyses upon all prediction scores displayed on this site you may download the file. Of the 15,633,440 scored yeast gene-function pairs, 6,368 genes have scores and 4,877 genes have at least one experimentally verified function.yeast, saccaromyces cerevisiae, s. cerevisiaeSCR_010561(YeastFunc, RRID:SCR_010561)University of Toronto; Ontario; Canada Last checked downnlx_38480http://func.med.harvard.edu/yeast/
Saccharomyces Genome Deletion ProjectResource, project portal, data or information resource, portal, databaseDatabase and project to reveal open reading frames (ORFs) in the yeast genome in order to discover their functions. A PCR-based gene deletion strategy is used to assign functions through phenotypic analysis of mutants.yeast, open reading frames, ORF, genome, deletion, Saccharomyces cerevisiaeSCR_014961(Saccharomyces Genome Deletion Project, RRID:SCR_014961)submitted by: Resource Identification PortalLast checked up
Yeast Search for Transcriptional Regulators And Consensus TrackingResource, data or information resource, databaseA curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references. It also includes the description of 326 specific DNA binding sites shared among 113 characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains a total of 7130 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database.yeast, gene, regulatory association, transcription factor, target gene, genomic, transcription regulation, transcription, web serviceSCR_006076(Yeast Search for Transcriptional Regulators And Consensus Tracking, RRID:SCR_006076)Fundacao para a Ciencia e a Tecnologiarelated to: SGD, Gene Ontology, Regulatory Sequence Analysis Tools, listed by: OMICtoolsReferences (4)Last checked upnif-0000-03652, OMICS_00547
mitopredResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution.yeast, c. elegans, drosophila, mouse, human, arabidopsisSCR_006135(mitopred, RRID:SCR_006135)University at Albany; New York; USA Last checked downnif-0000-03956
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