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| -- Sample queries for the ClinicalTrials.gov version-history sample dataset (DuckDB). | |
| -- | |
| -- Run them from the directory that holds the sample files (one folder per table, plus | |
| -- setup.sql). In the DuckDB CLI: | |
| -- .read setup.sql | |
| -- .read sample_queries.sql | |
| -- setup.sql creates one view per table, named after its folder ("core", "interventions", | |
| -- "results_outcome_measures", ...). | |
| -- | |
| -- Reading the data: | |
| -- * The dataset is a version history: nct_version numbers a trial's versions from 0, and | |
| -- nearly every table has one set of rows per (nct_id, nct_version). | |
| -- * There is no "current" flag. The current record is the highest nct_version held for an | |
| -- nct_id. That is the latest version in this dataset, which can be older than the live | |
| -- registry record if the trial has changed since it was last collected. | |
| -- * Every table ends with is_obsolete / obsolete_by: true when ClinicalTrials.gov now | |
| -- resolves the ID to a different registration. | |
| -- | |
| -- Each query starts with "-- name:" and "-- level:" lines; the blocks are independent. | |
| -- name: current_record | |
| -- level: basic | |
| -- The current record of every trial: one row per nct_id, its highest nct_version. | |
| SELECT nct_id, nct_version, overall_status, lead_sponsor_name, start_date, | |
| primary_completion_date, enrollment_count, last_update_post_date | |
| FROM core | |
| QUALIFY row_number() OVER (PARTITION BY nct_id ORDER BY nct_version DESC) = 1 | |
| ORDER BY nct_id; | |
| -- name: versions_per_trial | |
| -- level: basic | |
| -- How many versions each trial has, and the span of dates they were posted. | |
| SELECT nct_id, | |
| count(*) AS versions, | |
| min(last_update_post_date) AS first_posted, | |
| max(last_update_post_date) AS last_posted, | |
| count(DISTINCT overall_status) AS distinct_statuses | |
| FROM core | |
| GROUP BY nct_id | |
| ORDER BY versions DESC; | |
| -- name: status_changes_for_one_trial | |
| -- level: basic | |
| -- Every version of one trial in which the overall status changed. | |
| WITH v AS ( | |
| SELECT nct_id, nct_version, last_update_post_date, overall_status, | |
| lag(overall_status) OVER (PARTITION BY nct_id ORDER BY nct_version) AS previous_status | |
| FROM core | |
| WHERE nct_id = 'NCT03709680' | |
| ) | |
| SELECT nct_version, last_update_post_date, previous_status, overall_status | |
| FROM v | |
| WHERE previous_status IS DISTINCT FROM overall_status | |
| ORDER BY nct_version; | |
| -- name: current_interventions | |
| -- level: basic | |
| -- Interventions of each trial's current version (core joined to interventions on the | |
| -- two-column version key). | |
| WITH current AS ( | |
| SELECT nct_id, max(nct_version) AS nct_version FROM core GROUP BY nct_id | |
| ) | |
| SELECT c.nct_id, c.nct_version, i.intervention_type, i.intervention_name | |
| FROM current AS cur | |
| INNER JOIN core AS c ON c.nct_id = cur.nct_id AND c.nct_version = cur.nct_version | |
| INNER JOIN interventions AS i ON i.nct_id = c.nct_id AND i.nct_version = c.nct_version | |
| ORDER BY c.nct_id, i.intervention_type, i.intervention_name; | |
| -- name: current_trials_by_phase_and_status | |
| -- level: basic | |
| -- Current trials by phase and overall status. A trial with several phases (for example | |
| -- PHASE2 and PHASE3) counts once per phase. | |
| WITH current AS ( | |
| SELECT nct_id, max(nct_version) AS nct_version FROM core GROUP BY nct_id | |
| ) | |
| SELECT p.phase, c.overall_status, count(*) AS trials | |
| FROM current AS cur | |
| INNER JOIN core AS c ON c.nct_id = cur.nct_id AND c.nct_version = cur.nct_version | |
| INNER JOIN phases AS p ON p.nct_id = c.nct_id AND p.nct_version = c.nct_version | |
| GROUP BY p.phase, c.overall_status | |
| ORDER BY p.phase, trials DESC; | |
| -- name: trial_profile | |
| -- level: advanced | |
| -- One row per trial combining six tables at the current version. Each child table is | |
| -- aggregated to one row per trial first, so the joins cannot multiply rows. | |
| WITH current AS ( | |
| SELECT nct_id, max(nct_version) AS nct_version FROM core GROUP BY nct_id | |
| ), | |
| phase_agg AS ( | |
| SELECT nct_id, nct_version, string_agg(phase, ', ' ORDER BY phase) AS phases | |
| FROM phases GROUP BY nct_id, nct_version | |
| ), | |
| condition_agg AS ( | |
| SELECT nct_id, nct_version, count(*) AS conditions, | |
| string_agg(condition, '; ' ORDER BY condition) AS condition_list | |
| FROM conditions GROUP BY nct_id, nct_version | |
| ), | |
| intervention_agg AS ( | |
| SELECT nct_id, nct_version, count(*) AS interventions, | |
| string_agg(DISTINCT intervention_type, ', ') AS intervention_types | |
| FROM interventions GROUP BY nct_id, nct_version | |
| ), | |
| location_agg AS ( | |
| SELECT nct_id, nct_version, count(*) AS sites, count(DISTINCT country) AS countries | |
| FROM locations GROUP BY nct_id, nct_version | |
| ), | |
| collaborator_agg AS ( | |
| SELECT nct_id, nct_version, count(*) AS collaborators | |
| FROM collaborators GROUP BY nct_id, nct_version | |
| ) | |
| SELECT c.nct_id, c.overall_status, c.lead_sponsor_name, ph.phases, c.enrollment_count, | |
| cd.conditions, i.interventions, i.intervention_types, | |
| coalesce(l.sites, 0) AS sites, coalesce(l.countries, 0) AS countries, | |
| coalesce(co.collaborators, 0) AS collaborators | |
| FROM current AS cur | |
| INNER JOIN core AS c ON c.nct_id = cur.nct_id AND c.nct_version = cur.nct_version | |
| LEFT JOIN phase_agg AS ph ON ph.nct_id = c.nct_id AND ph.nct_version = c.nct_version | |
| LEFT JOIN condition_agg AS cd ON cd.nct_id = c.nct_id AND cd.nct_version = c.nct_version | |
| LEFT JOIN intervention_agg AS i ON i.nct_id = c.nct_id AND i.nct_version = c.nct_version | |
| LEFT JOIN location_agg AS l ON l.nct_id = c.nct_id AND l.nct_version = c.nct_version | |
| LEFT JOIN collaborator_agg AS co ON co.nct_id = c.nct_id AND co.nct_version = c.nct_version | |
| ORDER BY c.nct_id; | |
| -- name: registry_as_of_date | |
| -- level: advanced | |
| -- What the registry said about each trial on a past date: the latest version posted on or | |
| -- before that date, with its conditions, compared with today's status. Change as_of below. | |
| WITH params AS ( | |
| SELECT DATE '2019-01-01' AS as_of | |
| ), | |
| as_of_version AS ( | |
| SELECT c.nct_id, c.nct_version | |
| FROM core AS c | |
| CROSS JOIN params AS p | |
| WHERE c.last_update_post_date <= p.as_of | |
| QUALIFY row_number() OVER (PARTITION BY c.nct_id ORDER BY c.nct_version DESC) = 1 | |
| ), | |
| current AS ( | |
| SELECT nct_id, max(nct_version) AS nct_version FROM core GROUP BY nct_id | |
| ), | |
| condition_agg AS ( | |
| SELECT nct_id, nct_version, string_agg(condition, '; ' ORDER BY condition) AS conditions | |
| FROM conditions GROUP BY nct_id, nct_version | |
| ) | |
| SELECT then_.nct_id, then_.nct_version AS version_then, then_.overall_status AS status_then, | |
| then_.primary_completion_date AS primary_completion_then, cd.conditions AS conditions_then, | |
| now_.nct_version AS version_now, now_.overall_status AS status_now, | |
| now_.primary_completion_date AS primary_completion_now | |
| FROM as_of_version AS a | |
| INNER JOIN core AS then_ ON then_.nct_id = a.nct_id AND then_.nct_version = a.nct_version | |
| LEFT JOIN condition_agg AS cd ON cd.nct_id = then_.nct_id AND cd.nct_version = then_.nct_version | |
| INNER JOIN current AS cur ON cur.nct_id = then_.nct_id | |
| INNER JOIN core AS now_ ON now_.nct_id = cur.nct_id AND now_.nct_version = cur.nct_version | |
| ORDER BY then_.nct_id; | |
| -- name: primary_completion_date_slips_by_phase | |
| -- level: advanced | |
| -- How often sponsors push out a trial's primary completion date, by phase. Each version is | |
| -- compared with the one before it (core), dated from version_history (ct_gov_version equals | |
| -- nct_version) and attributed to the phases of the version that made the change. | |
| -- A trial with several phases counts once per phase. Days are gross: a date moved earlier | |
| -- and later again counts each push. | |
| WITH dated AS ( | |
| SELECT c.nct_id, c.nct_version, c.primary_completion_date, | |
| lag(c.primary_completion_date) OVER (PARTITION BY c.nct_id ORDER BY c.nct_version) | |
| AS previous_date, | |
| h.change_date | |
| FROM core AS c | |
| INNER JOIN version_history AS h | |
| ON h.nct_id = c.nct_id AND h.ct_gov_version = c.nct_version | |
| ), | |
| slips AS ( | |
| SELECT *, date_diff('day', previous_date, primary_completion_date) AS slip_days | |
| FROM dated | |
| WHERE primary_completion_date > previous_date | |
| ) | |
| SELECT p.phase, | |
| count(DISTINCT s.nct_id) AS trials_pushed, | |
| count(*) AS pushes, | |
| round(avg(s.slip_days)) AS avg_days_per_push, | |
| max(s.slip_days) AS longest_push_days, | |
| min(s.change_date) AS first_push_posted, | |
| max(s.change_date) AS last_push_posted | |
| FROM slips AS s | |
| INNER JOIN phases AS p ON p.nct_id = s.nct_id AND p.nct_version = s.nct_version | |
| GROUP BY p.phase | |
| ORDER BY pushes DESC; | |
| -- name: primary_outcome_results | |
| -- level: advanced | |
| -- Reported results for primary outcomes at the current version: outcome, group, category | |
| -- and measured value. Joins five tables through the outcome / class / category ordinals. | |
| WITH current AS ( | |
| SELECT nct_id, max(nct_version) AS nct_version FROM core GROUP BY nct_id | |
| ) | |
| SELECT om.nct_id, om.title AS outcome, om.unit_of_measure, | |
| g.title AS group_title, cat.title AS category, ms.value, ms.spread | |
| FROM current AS cur | |
| INNER JOIN results_outcome_measures AS om | |
| ON om.nct_id = cur.nct_id AND om.nct_version = cur.nct_version AND om.type = 'PRIMARY' | |
| INNER JOIN results_outcome_classes AS cl | |
| ON cl.nct_id = om.nct_id AND cl.nct_version = om.nct_version AND cl.outcome_ord = om.outcome_ord | |
| INNER JOIN results_outcome_categories AS cat | |
| ON cat.nct_id = cl.nct_id AND cat.nct_version = cl.nct_version | |
| AND cat.outcome_ord = cl.outcome_ord AND cat.class_ord = cl.class_ord | |
| INNER JOIN results_outcome_measurements AS ms | |
| ON ms.nct_id = cat.nct_id AND ms.nct_version = cat.nct_version | |
| AND ms.outcome_ord = cat.outcome_ord AND ms.class_ord = cat.class_ord | |
| AND ms.category_ord = cat.category_ord | |
| INNER JOIN results_outcome_groups AS g | |
| ON g.nct_id = ms.nct_id AND g.nct_version = ms.nct_version | |
| AND g.outcome_ord = ms.outcome_ord AND g.group_id = ms.group_id | |
| ORDER BY om.nct_id, om.outcome_ord, cl.class_ord, cat.category_ord, g.group_id; | |
| -- name: serious_adverse_event_rates_by_group | |
| -- level: advanced | |
| -- Serious adverse events at the current version: for each trial, arm group and event term, | |
| -- how many participants were affected out of those at risk (events, event stats and groups). | |
| WITH current AS ( | |
| SELECT nct_id, max(nct_version) AS nct_version FROM core GROUP BY nct_id | |
| ) | |
| SELECT e.nct_id, g.title AS group_title, e.organ_system, e.term, | |
| s.num_affected, s.num_at_risk, | |
| round(100.0 * s.num_affected / nullif(s.num_at_risk, 0), 2) AS pct_affected | |
| FROM current AS cur | |
| INNER JOIN results_adverse_serious_events AS e | |
| ON e.nct_id = cur.nct_id AND e.nct_version = cur.nct_version | |
| INNER JOIN results_adverse_serious_event_stats AS s | |
| ON s.nct_id = e.nct_id AND s.nct_version = e.nct_version AND s.event_ord = e.event_ord | |
| INNER JOIN results_adverse_event_groups AS g | |
| ON g.nct_id = s.nct_id AND g.nct_version = s.nct_version AND g.group_id = s.group_id | |
| WHERE s.num_affected > 0 | |
| ORDER BY pct_affected DESC, e.nct_id, e.term | |
| LIMIT 50; | |
| -- name: arms_and_their_interventions | |
| -- level: advanced | |
| -- Which intervention each study arm receives, at the current version (arm_groups joined to | |
| -- the arm/intervention link table and to interventions for the description). | |
| WITH current AS ( | |
| SELECT nct_id, max(nct_version) AS nct_version FROM core GROUP BY nct_id | |
| ) | |
| SELECT a.nct_id, a.arm_label, a.arm_type, i.intervention_type, i.intervention_name | |
| FROM current AS cur | |
| INNER JOIN arm_groups AS a ON a.nct_id = cur.nct_id AND a.nct_version = cur.nct_version | |
| INNER JOIN intervention_arm_links AS l | |
| ON l.nct_id = a.nct_id AND l.nct_version = a.nct_version AND l.arm_label = a.arm_label | |
| INNER JOIN interventions AS i | |
| ON i.nct_id = l.nct_id AND i.nct_version = l.nct_version | |
| AND i.intervention_name = l.intervention_name AND i.intervention_type = l.intervention_type | |
| ORDER BY a.nct_id, a.arm_label, i.intervention_name; | |
| -- name: sponsor_site_footprint | |
| -- level: advanced | |
| -- Each lead sponsor's current trials and where they run: trials, sites and countries | |
| -- (core joined to locations at the current version). | |
| WITH current AS ( | |
| SELECT nct_id, max(nct_version) AS nct_version FROM core GROUP BY nct_id | |
| ) | |
| SELECT c.lead_sponsor_name, | |
| count(DISTINCT c.nct_id) AS trials, | |
| count(*) AS sites, | |
| count(DISTINCT l.country) AS countries | |
| FROM current AS cur | |
| INNER JOIN core AS c ON c.nct_id = cur.nct_id AND c.nct_version = cur.nct_version | |
| INNER JOIN locations AS l ON l.nct_id = c.nct_id AND l.nct_version = c.nct_version | |
| GROUP BY c.lead_sponsor_name | |
| ORDER BY sites DESC; | |