Gen3 - Managing Timepoints

Managing Timepoints in a Submission


Some elements of submitted datasets can be related to each other in terms of time. To stay in compliance with HIPAA, Gen3 commons create timelines without using real dates. Every other date field is anchored by the “index_date” in the “case” node.

In this field, dates for events such as “Study Enrollment” or “Diagnosis” can be entered. For more information about the index_date field please go to the case node in the dictionary, https://data.mycommons.org/dd/case.

NOTE: For these user guides, https://data.mycommons.org is an example URL and will not be the actual URL of the data commons.

Examples of Submissions Using Multiple Date Times

Patient A enrolls in a study on July 1, and has a sample taken on July 10. For patient A:

  • case.index_date = “Study Enrollment”

  • biospecimen.days_to_procurement = July 10 - July 1 = 9

Alternatively if patient A was diagnosed 2 years before the study began, the index_date for “Diagnosis” would be treated like this:

  • case.index_date = “Diagnosis”

  • biospecimen.days_to_procurment = July 10, 2017 - July 1, 2015 = 739

Negative Dates

Days to values can also be negative. If an index_date event occurs after the event, the days_to values would be presented as negative.

If Patient A had a biospecimen taken when they were initially diagnosed:

  • case.index_date = “Study Enrollment”

  • biospecimen.days_to_procurement = July 10, 2015 - July 1, 2017 = -721

No Time Series

The days_to_procurement and days_to_collection are required fields. If there are no data available, Gen3 commons allow escape values of “Unknown” and “Not Applicable”. Please use “Unknown” in the instances where there is an established time series, but are unable to note the date of the event. Use “Not Applicable” if there is no time series at all.

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