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Pair (data model entity)

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

In the FireCloud data model, a Pair entity represents a pair of biological samples collected from a Participant, for example a tumor sample and a normal sample from a cancer patient. The Pair metadata should be structured as follows:

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

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

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


Example of Pair metadata load file

entity:pair_id case_sample_id control_sample_id participant_id
TCGA-5M-AAT4_p1 TCGA-5M-AAT4-01A TCGA-5M-AAT4-10A TCGA-5M-AAT4
TCGA-NH-A8F8-p1 TCGA-NH-A8F8-01A TCGA-NH-A8F8-10A TCGA-NH-A8F8
Post edited by Geraldine_VdAuwera on
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