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Trio of Timepoint Files

Trio of Timepoint Files

For longitudinal studies submitting samples AND data from the same subject on multiple different dates, there are 3 Timepoint Files that must be submitted together with the rest of the submission package. The filenames preceding the file suffixes (ie _tp_phen) should be identical for all 3 files.

  1. Timepoint Definition (FILENAME_tp) — analogous to the _dx file, this file defines the timecodes to be used in the _tp_phen file
  2. Timepoint Phenotypic File (FILENAME_tp_phen) — This file defines the actual data whose format is defined in the Timepoint Phenotypic Data Dictionary File (_tp_phen_dd) (see below).
  3. Timepoint Phenotypic Data Dictionary File (FILENAME_tp_phen_dd) — This file defines the format of the data that will reside in the accompanying timepoint phenotypic file. There are 4 mandatory fields that must appear first in the file. We encourage users to customize the timepoint data dictionary (and, of course, the corresponding timepoint phenotypic file) to include additional clinical information beyond the 4 core fields. This can be done according to the highly flexible format-definition language outlined on the Data Dictionary File page. See Data Dictionary File.

Timepoint File (FILENAME_tp)

Column Name Type Format / Value Checks Additional Comments
study_id integer(3)

Definition: Study ID assigned by NIMH.

timecode string

Definition: Definition: Study ID assigned by NIMH Definition: A short code that signifies a meaningful event during a clinical evaluation.

Sample Value: T1

definition string

Definition: A compact explanation of each timecode.

Sample Value: baseline

description string

Definition: An expanded explanation of each timecode.

Sample Value: Sample taken from subject upon enrollment in study prior to treatment

Timepoint Phenotypic File (FILENAME_tp_phen)

Column Name Type Format / Value Checks Additional Comments
ind_id string

Checks:

Must match exactly with Subject Code submitted to RUCDR.

Field is a required field and cannot be left empty.

Values in the (ind_id, timepoint) fields should be unique.

Values in the (ind_id, ruid, timepoint) fields should be unique.

Definition: The unique individual id submitted to RUCDR with the biosample.

Comments: IMPORTANT — This id is used to verify subject \ RUID pairs at RUCDR. Therefore, the id you submit here should match exactly the subject-code submitted to RUCDR.

ruid string

Checks:

Values in the ruid field should be unique.

Values in the (ind_id, ruid, timepoint) fields should be unique.

Definition: RUCDR sample id, "RUID".

Sample Value: 03C19340

Empty string is considered an invalid value

Empty strings should be represented with the value NULL

timecode string

Checks:

Field is a required field and cannot be left empty.

Values in the (ind_id, timecode) fields should be unique.

Values in the (ind_id, ruid, timecode) fields should be unique.

Definition: A unique, short code used to represent a timepoint, defined in the _tp file.

Sample Value: T0

timepoint_date date

Checks:

Cannot be left empty

Record dates in YYYY-MM-DD format (ISO_8601 Dates)

Definition: The date corresponding to the timepoint for an individual.

Sample Value: 2016-01-01