server cgi for Beacon+ development
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beaconPlus
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README.md
beacondeliver.cgi
beaconhandover.cgi
beaconinfo.cgi
beaconontologies.cgi
beaconresponse.cgi

README.md

BeaconResponse - a Perl CGI for Beacon+ queries on GA4GH compatible databases

Query parameters

  • datasetId
    • the dataset to be queried
    • example: arraymap, which will expand to arraymap_ga4gh as database name
    • default: arraymap
  • assemblyId
    • the genome assembly
    • example: GRCh38

Database naming

The script uses some naming conventions for databases and collections:

  • MongoDB database (in our implementation)
    • datasetId_ga4gh
  • collections
    • individuals
    • biosamples
    • callsets
    • variants

Example use, web call:

SNV query on dataset "dipg" with phenotype response:

CNV query (defaults do dataset "arraymap") with bio-metadata component and phenotype response: