ClinGen Allele Registry

The ClinGen Allele Registry provides unique variant identifiers both programmatically (via APIs) and via this search interface. If a variant is not present in the Registry, authorized users may register the variant and get an identifier within seconds. The variants are automatically mapped across known reference sequences and to identifiers from major variant databases. The current content of the Registry is searchable using HGVS expressions representing nucleic acid or amino acid variants across more than 500,000 reference sequences (genome assemblies, transcripts, amino acid sequences). Alleles can be also queried by locus, gene and ClinVar or dbSNP identifiers. The registry regularly imports variants from ExAC, ClinVar and other databases. To facilitate wide integration of the registry services with existing software and workflows for variant evaluation, e.g. Pathogenicity Calculator, all the functionalities of the registry are exposed via REST APIs. The API also allows for bulk query and registration of variants. Hundreds of variants saved as HGVS expressions can be processed as a batch in less than ten seconds. This will also be extended to VCF file in the near future. For instructions on how to register large batches of variants, follow the "API specification" provided on the home page. To register new alleles in the Allele Registry, you will need a valid login and password. To create a login, please send an email request to brl-allele-reg@bcm.edu with a preferred login name. If you have any questions, please do not hesitate to contact brl-allele-reg@bcm.edu.

Tags: ClinGen CAR Variants Canonical IDs Allele Registry Naming Service

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Digital Object Assessments (2)


Assessment Metrics Date
Rubric Project   The service has a landing page and accessible The service has a global unique identifier The service has an unique name and an informative description The service can be freely downloaded or accessed from a webpage The service utilizes a community-accepted nomenclature Tutorials for the service are available on the homepage Licensing information is provided on the homepage Versions of the service are displayed on the homepage Contact information is provided for the creator(s) of the service and information describing how to cite the service is provided The service can be accessed programmatically Machine readable data A standardized ID or accession number is used to identify the dataset Does your resource create and host data or knowledge assets that can be accessed by researchers? Does your resource create and host software assets that can be downloaded or installed and then used by researchers? Does your resource maintain a Web site that can be accessed by researchers? Does your resource perform expert manual or automated data or knowledge curation? Does your resource accept data submissions from researchers? Does your software read and write data using widely used community standards or formats? What sorts of documentation do you provide for your software? Where does your resource host your software for development? Check all the boxes that apply Are your repositories public or private? Where does your resource host your software for download? Check all the boxes that apply. What main languages are used in the software you offer to the public? Check all the boxes that apply. Do you foresee a need to migrate some or all of your code to other software languages in the foreseeable future? What other software language(s) would you migrate some or all of your code to? Check all the boxes that apply. Is your software available as a downloadable container? Does your resource release versioned software packages? Do you provide documentation describing each software release? Do you provide standard metadata describing each software release? What general approaches does your resource take for curation? Check all the boxes that apply. Do your curation methods introduce standard terms from public ontologies or vocabularies into the curated content? Do your curation methods add citations of relevant publications into the curated content? Do you support community curation, or curation by experts outside of your resource? Do you display detailed provenance that indicates that the curation was made by the community or external experts? Do you require specific file formats for submission to your resource? What specific file formats are required for submission to your resource? Check all the boxes that apply. Are terms from specific vocabularies or ontologies required in submissions to your resource? What specific vocabularies or ontologies are used or required in submissions to your resource? Check all boxes that apply. Are specific database identifiers required in submissions to your resource? Does your resource have mechanisms to record the origin and chain of custody of the submissions? Does your resource ascertain if submitters have obtained all necessary ethical and legal approvals for data sharing and publication? How frequently are submissions released to the public? Do you have embargo or Hold Until Publication policies for submissions? What processes are used to validate submissions? Check all the boxes that apply. Do you plan to start accepting data submissions from researchers as part of the new NIH Data Management and Sharing (DMS) policy? Have you ever performed a FAIR assessment of your assets using some tool or rubric? For example, FAIRshake, FAIR-Checker, or GO FAIR. Do you assign unique, persistent identifiers to some or all of your assets? What kind of unique identifiers do you assign? Check all the boxes that apply. What kinds of assets receive these unique, persistent identifiers in your resource? Does your resource describe its assets using any public metadata standards? For example, DataCite, OpenAIRE, Dublin Core. Does your resource annotate its assets with its own custom metadata vocabulary? What are the public metadata standards that you apply? Check all the boxes that apply. Does your resource annotate its assets with its own custom metadata vocabulary?
BRL Resource FAIRness Metrics NHGRI FAIR Assessment for BRL ClinGen Tools
yes (1.00)                                                                                                         Jan 26, 2024
NHGRI FAIR Assessment 2024 Rubric NHGRI FAIR Assessment for BRL ClinGen Tools
                                                                                                          Jan 26, 2024