This file is delivered to each HPO after a submission is uploaded and processed by the Curation pipeline. It contains preliminary information about the submission and its data quality results. Use the sections below to interpret the contents.
File Summary
Shows whether the submitted files were:
found,
parsed, and
loaded successfully by the Curation pipeline.
Errors & Warnings
Lists file format errors and warnings identified in the submission.
Action required: Fix all errors, then re-run the submission.
Warnings should be reviewed and addressed when possible.
Data Quality Report
Includes the following subsections:
New Feature
What it is
This report provides summary statistics for the submission. It is an aggregated view of the participant-level report written to the bucket as participant_stats.csv.
Why it matters
It helps interpret and compute Data Transfer Rates in the Tableau dashboard (NIH Grant Award Metrics), including the “in-person visit” logic used for Data Transfer Rate C .
How to interpret participant_stats.csv
| person_id | ehr_data_available | hpo_paired_participant | OGANIZATION | ehr_consent_yes_flag | patient_status | pm_status | bbo_collection_status |
| 1 | 1 | 1 | SAME_PAIRED_ORG | 1 | 1 | 1 | 1 |
| 2 | 1 | 0 | OTHER_PAIRED_ORG | 1 | 0 | 1 | 1 |
- person_id: the participant identifier (PMID).
-
ehr_data_available:
1if at least one EHR record is present in the submission (beyond thepersontable). -
hpo_paired_participant:
1if the participant is paired with the submitting HPO. -
ORGANIZATION:
SAME_PAIRED_ORGif the participant is paired with the submitting ORGOTHER_PAIRED_ORGotherwise
ehr_consent_yes_flag:
1if the participant has valid EHR consent.patient_status:
1if patient status equals"YES".
Note: This applies to legacy data only, since PPSC has not provided a channel for HPOs to upload patient status.pm_status:
1if the participant has completed physical measurements.bbo_collection_status:
1if the participant completed onsite biospecimen collection.
In-person visit logic (used in the dashboard)
A participant is considered to have an in-person visit if:
pm_status = 1 OR bbo_collection_status = 1
This logic is used to define Data Transfer Rate C in the Tableau dashboard.
Data Completness
Shows completeness for each OMOP table. Rows with NULL or 0 concept_id values are counted toward incompleteness.
Drug Concept Mapping Percentages
Shows concept mapping coverage for major drug classes.
Lab Concept Summary
Lists common lab concepts and whether records were found in the measurement table. Coverage does not need to be 100%.