Beacon - Search

The GA4GH (Global Alliance for Genomics and & Health) Beacon Projectis a project to encourage international sites to share genetic data in the simplest of all technical contexts. The service is designed merely to accept a query of the form "Do you have any genomes with an 'A' at position 100,735 on chromosome 3" (or similar data) and responds with one of "Yes" or "No."

The Beacon Network lists all the known beacons.

For programmatic access to the COSMIC beacon, the minimal URL for the request is: http://cancer.sanger.ac.uk/api/ga4gh/beacon/query?chrom=?;pos=?;allele=?

Query Parameters

Required:

chrom
Chromosome name - either 1-22, X, Y or MT
pos
1-based position - a positive integer (not greater than length of chromosome)
allele
Mutant Allele - 'A', 'C', 'G', 'T', 'I' (insertion) or 'D' (deletion)

Optional:

ref
Genome Assembly - GRCh28 (default), or GRCh27
dataset
Data Source - cosmic (default),cell_lines (Cell Lines Project) or wgs (Whole Genomes)
format
Data Format - text (default), json or xml

Response (text)

'Yes'
Allele observed in dataset
'No'
Allele not observed in dataset
'Error'
Error retrieving data from data source.

Response (json)

{ 'response':{'exists':'true'} }
Allele observed in dataset
{ 'response':{'exists':'false'} }
Allele not observed in dataset, but other mutant alleles exist
{ 'response':{'exists':'null'} }
No mutant alleles observed in dataset
{ 'response':{'exists':'null','error':'message'} }
Error retrieving data from data source

Response (xml)

<response exists="true">
Allele observed in dataset
<response exists="false">
Allele not observed in dataset, but other mutant alleles exist
<response exists="null">
No mutant alleles observed in dataset
<response exists="null" error="message">
Error retrieving data from data source

Usage Notes:

Please be considerate to other users of the Beacon and other services hosted at the Wellcome Trust Sanger Institute. We reserve the right to throttle/block any usage which adversly affects this and other services hosted on the same hardware.

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