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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
Human Genome Variation Society: Databases and Other ToolsResource, data set, data or information resourceA list of various databases freely available to the public, including several mutation and variation resources, such as education resources for teachers students provided by the Human Genome Variation Society. Databases listed include: * Locus Specific Mutation Databases * Disease Centered Central Mutation Databases * Central Mutation and SNP Databases * National and Ethnic Mutation Databases * Mitochondrial Mutation Databases * Chromosomal Variation Databases * Other Mutation Databases ( i.e. your round holes don''''t fit our square pegs) * Clinical and Patient Aspects Databases * Non Human Mutation Databases * Artificial Mutations Only * Other Related Databases * Education Resources for Teachers and Studentsgenome, artificial, chromosome, clinical, disease, human, mitochondrial, non human, snp, mutation, genetic variation, education, ethnicSCR_006876(Human Genome Variation Society: Databases and Other Tools, RRID:SCR_006876)Human Genome Variation Society related to: Monarch InitiativeLast checked downnif-0000-02959
openSNPResource, source code, database, service resource, storage service resource, software resource, data repository, data or information resourceDatabase of raw data from people who have shared their direct-to-customer (DTC) genetic results from 23andMe, deCODEme or FamilyTreeDNA. Logged-In users can search the database for users with specific phenotypes and mass-download all corresponding SNP-datasets. This allows you to get datasets like All genotyping files of openSNP-users that have Alzheimer and the corresponding control group. They are currently working on providing API-access. You can also use JSON to get access to openSNP-data and some other ways: If you want to automate the file-downloads for a given phenotype the RSS-feeds could help you. Inside the RSS-XML there are 2 flags you could use to automatically create correct genotype-groups: gives you the variation of this user at the phenotype you are looking at and gives you the download link. If you were genotyped by 23andMe, deCODEme or FamilyTreeDNA (contact them regarding others) you can upload the raw genotype data which you can download from your DTC test provider. The data will then be openly available for the world to see and download. They also parse these SNPs and annotate them. For annotation they include the manually curated SNPedia and find Open Access primary publications which appear in the journals of The Public Library of Science (PLoS), an Open Access publishing group. Additionally they screen Mendeley, a crowd-sourced repository of scientific publications. You can also publish some of your phenotypes so some day it might get possible to associate some SNPs with phenotypes. You can also share your knowledge about SNPs and phenotypes with other users and can socialize.SNP, genotype, phenotype, snp, genetic variation, disease, trait, genetics, genome wide association study, crowdsourcing, data setSCR_001636(openSNP, RRID:SCR_001636)related to: Monarch InitiativeLast checked upnlx_153904
Leiden Open Variation DatabaseResource, data processing software, database, software application, data storage software, service resource, storage service resource, software resource, data repository, data or information resourceFreely available tool for Gene-centered collection and display of DNA variations. It also provides patient-centered data storage and storage of Next Generation Sequencing (NGS) data, even of variants outside of genes. Please note that LOVD provides a system for storage of information on genes and allelic variants. To obtain information about any genes or variants, do not download the LOVD package. This information should be obtained from the respective databases, http://www.lovd.nl/2.0/index_list.php In total: 2,507,027 variants (2,208,937 unique) in 170,935 individuals in 62619 genes in 88 LOVD installations. (Aug. 2013) LOVD 3.0 shared installation, http://databases.lovd.nl/shared/genes To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer. You can download LOVD in ZIP and GZIPped TARball formats.genetic variation, genomic variant, gene, transcript, disease, next generation sequencing, dna variation, variant, clinical, screening, locus, phenotype, sequence variation, allelic variant, data sharingSCR_006566(Leiden Open Variation Database, RRID:SCR_006566)Leiden University; Leiden; Netherlands European Union FP7related to: Monarch Initiative, listed by: OMICtoolsReferences (2)Last checked upnif-0000-02998, OMICS_00275
Human Variation DBResource, service resource, data or information resource, data repository, storage service resource, databaseA repository database to achieve continuous and intensive management of GWAS data and variation data identified by next generation sequencing (NGS) and data-sharing among researchers. In this database, variations including short/long insertions / deletions and structural variations related to disease susceptibility, virus resistance, and drug response are registered along with statistical genetic results and simple clinical characteristics to clarify the locus specific characteristics. Currently this database contains information extracted from scientific papers and next generation sequencing results and other small scale experimental results of several research laboratories. Mutation data submission is greatly appreciated.gene, genome, disease, snp, next generation sequencing, gwas, genetic variation, mutation, copy number variation, insertion, deletion, structural variationSCR_009014(Human Variation DB, RRID:SCR_009014)NBDC - National Bioscience Database Center Japan Science and Technology Agencyrelated to: Monarch InitiativeReferences (2)Last checked upnlx_153886
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