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Sample (data model entity)

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
edited June 2017 in Dictionary

In the FireCloud data model, a Sample entity represents a biological sample collected from a participant, which may be associated with one or more sequencing runs, for example. The sample metadata should be structured as follows:

  • first column: entity:sample_id (key)
  • subsequent columns (no ordering requirement):

    • participant_id (foreign key)
    • entity attributes
  • exactly one row per entity in the file

Note that you should always load participant metadata before attempting to load additional entities such as samples that refer to the participants.

Example of Sample metadata load file

entity:sample_id participant_id sample_type
TCGA-5M-AAT4-01A TCGA-5M-AAT4 primary_solid_tumor
TCGA-5M-AAT4-10A TCGA-5M-AAT4 blood_derived_normal
TCGA-NH-A8F8-01A TCGA-NH-A8F8 primary_solid_tumor
TCGA-NH-A8F8-10A TCGA-NH-A8F8 blood-derived_normal
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