FireCloud is now powered by Terra! -- STARTING MAY 1st, 2019 THIS WEBPAGE WILL NO LONGER BE UPDATED.
From now on, please visit the Terra Help Center for documentation, tutorials, roadmap and feature announcements.
Want to talk to a human? Email the helpdesk, post feature requests or chat with peers in the community forum.
FIRECLOUD | Doc #9772 | Pair (data model entity)

Pair (data model entity)
Dictionary | Created 2017-06-14 | Last updated 2017-07-22


Comments (0)

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

Return to top Comment on this article