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ga4gh-beacon / specification

GA4GH Beacon specification.
Apache License 2.0
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Genotype + Phenotype Query language #26

Open mfiume opened 8 years ago

mfiume commented 8 years ago

Consider using the individual, sample, metadata, and variant core APIs as templates for a genotype + phenotype query language.

For example, we can ask for information about alleles in a specific cohort of inidivuals:

query: { genome.assembly : GRCh37, genome.chrom : 13, genome.position : 32936732, genome.allele: C, individual.sex : ‘F’, individual.age : <30, individual.disease.stage : ‘metastatic’ individual.disease.name : ‘breast cancer’ }

means, what are the properties of this allele in females under 30 with metastatic breast cancer? The beacon could say,

response : { exists : true, metadata : { frequency: 0.2 } }

where the metadata represents the information aggregated only on the specific subpopulation queried.

saifGeL commented 6 years ago

This has large security implications for identifiability.