Standard domain set

The standard domain set is the 4 tables a study supplies to safety.viz. Their column names are the ADaM-shaped defaults the charts already expect, so data in this shape feeds all 17 charts without renaming a column, and a column under another name is mapped through that chart's settings.

Domains: Subject-level, Adverse events, Labs and vitals, ECG
Charts: 17 read the standard set
Manifest: portfolio.jsonThe file this page is generated from, described by its JSON Schema, in format version 2

Subject-level `subject`

One row per participant.

Demo extract: adsl.csv
Charts it feeds: Time-to-Event Explorer
Charts that add it when it is supplied: Group comparison, Association scatter, Correlation matrix, Biomarker screen

Column	Label	What it holds
`USUBJID`	Participant	Unique participant identifier; the key that joins every domain.
`ARM`	Treatment arm	Treatment group the participant was assigned to.
`SITEID`	Site	Investigational site identifier.
`SEX`	Sex	Participant sex.
`RACE`	Race	Participant race.
`EOSDY`	End-of-study day	Study day follow-up ended (day 1 = first dose); the censoring time for participants with no event.
`EOSSTT`	End-of-study status	End-of-study status, shown where a participant is censored.

Adverse events `ae`

One row per adverse event, plus one all-blank placeholder row per participant with no events.

Demo extract: adae.csv
Charts it feeds: Adverse Event Explorer, Adverse Event Timelines, Time-to-Event Explorer
Charts that add it when it is supplied: Participant Profile

Column	Label	What it holds
`USUBJID`	Participant	Unique participant identifier.
`AESEQ`	Sequence	Sequence number of the event within the participant.
`AEBODSYS`	Body system	System organ class of the event.
`AEDECOD`	Preferred term	Dictionary-coded preferred term.
`AETERM`	Reported term	Verbatim term as reported.
`ASTDY`	Start day	Study day the event started (day 1 = first dose).
`AENDY`	End day	Study day the event ended.
`ARM`	Treatment arm	Treatment group the participant was assigned to.
`AESEV`	Severity	Severity or intensity of the event.
`AESER`	Serious	Whether the event was serious (Y/N).

Labs and vitals `bds`

One row per participant, measure and visit: laboratory results and vital signs together, in long format.

Demo extract: adbds.csv
Charts it feeds: Safety Histogram, Safety Outlier Explorer, Safety Results Over Time, Safety Shift Plot, Safety Delta-Delta, Hepatic Safety Explorer, Hepatic ALT Waterfall, Nephrotoxicity Explorer, Participant Profile, Group comparison, Association scatter, Correlation matrix, Biomarker screen

Column	Label	What it holds
`USUBJID`	Participant	Unique participant identifier.
`TEST`	Measure	Name of the laboratory test or vital sign.
`STRESN`	Result	Numeric result in standard units.
`STRESU`	Unit	Standard unit of the result.
`STNRLO`	Lower limit of normal	Lower limit of the normal range.
`STNRHI`	Upper limit of normal	Upper limit of the normal range.
`VISIT`	Visit	Visit name.
`VISITNUM`	Visit order	Numeric visit order.
`DY`	Study day	Study day of the measurement (day 1 = first dose).
`ARM`	Treatment arm	Treatment group the participant was assigned to.
`SITEID`	Site	Investigational site identifier.
`SEX`	Sex	Participant sex.
`RACE`	Race	Participant race.

ECG `eg`

One row per participant, ECG interval and visit, in long format.

Demo extract: adeg.csv
Charts it feeds: QT Safety Explorer

Column	Label	What it holds
`USUBJID`	Participant	Unique participant identifier.
`TEST`	Measure	Name of the ECG interval or parameter.
`STRESN`	Result	Numeric result in standard units.
`STRESU`	Unit	Standard unit of the result.
`BASE`	Baseline value	The participant’s baseline value for the measure.
`CHG`	Change from baseline	Result minus baseline.
`ABLFL`	Baseline flag	Marks the baseline record (Y).
`ARM`	Treatment arm	Treatment group the participant was assigned to.
`VISIT`	Visit	Visit name.
`VISITNUM`	Visit order	Numeric visit order.

What each chart needs

Each setting names the column a chart reads for one purpose, and defaults to the column shown. Required marks the settings the chart's own data schema lists as required; the rest are optional. A setting shown with no default reads no column until one is named, and the chart's API reference says what each setting does.

Safety Histogram

Live demo · API reference · Data schema

Reads: Labs and vitals

Setting	Required	Default column	What it holds	Read from
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`id_col`	optional	`USUBJID`	Participant	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`normal_col_low`	optional	`STNRLO`	Lower limit of normal	Labs and vitals
`normal_col_high`	optional	`STNRHI`	Upper limit of normal	Labs and vitals

Safety Outlier Explorer

Live demo · API reference · Data schema

Reads: Labs and vitals

Setting	Required	Default column	What it holds	Read from
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`id_col`	optional	`USUBJID`	Participant	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`normal_col_low`	optional	`STNRLO`	Lower limit of normal	Labs and vitals
`normal_col_high`	optional	`STNRHI`	Upper limit of normal	Labs and vitals

Safety Results Over Time

Live demo · API reference · Data schema

Reads: Labs and vitals

Setting	Required	Default column	What it holds	Read from
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`time_col`	required	`VISIT`	Visit	Labs and vitals
`time_order_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`id_col`	optional	`USUBJID`	Participant	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals

Safety Shift Plot

Live demo · API reference · Data schema

Reads: Labs and vitals

Setting	Required	Default column	What it holds	Read from
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`visit_col`	required	`VISIT`	Visit	Labs and vitals
`visit_order_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`id_col`	optional	`USUBJID`	Participant	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals

Safety Delta-Delta

Live demo · API reference · Data schema

Reads: Labs and vitals

Setting	Required	Default column	What it holds	Read from
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`id_col`	required	`USUBJID`	Participant	Labs and vitals
`visit_col`	required	`VISIT`	Visit	Labs and vitals
`visitn_col`	optional	`VISITNUM`	Visit order	Labs and vitals

Hepatic Safety Explorer

Live demo · API reference · Data schema

Reads: Labs and vitals

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Labs and vitals
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`normal_col_high`	required	`STNRHI`	Upper limit of normal	Labs and vitals
`normal_col_low`	optional	`STNRLO`	Lower limit of normal	Labs and vitals
`studyday_col`	optional	`DY`	Study day	Labs and vitals
`visit_col`	optional	`VISIT`	Visit	Labs and vitals
`visitn_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`arm_col`	optional	`ARM`	Treatment arm	Labs and vitals
`baseline_col`	optional	No default	—	Labs and vitals

Hepatic ALT Waterfall

Live demo · API reference · Data schema

Reads: Labs and vitals

Meaningful for a cohort enrolled with elevated baseline ALT and normal baseline bilirubin; the demo site draws it on the synthetic abnormal-baseline extract adbds-abnbl.csv, which has the same columns as the labs and vitals domain.

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Labs and vitals
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`normal_col_high`	required	`STNRHI`	Upper limit of normal	Labs and vitals
`normal_col_low`	optional	`STNRLO`	Lower limit of normal	Labs and vitals
`studyday_col`	optional	`DY`	Study day	Labs and vitals
`visit_col`	optional	`VISIT`	Visit	Labs and vitals
`visitn_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`arm_col`	required	`ARM`	Treatment arm	Labs and vitals
`baseline_col`	optional	No default	—	Labs and vitals

Nephrotoxicity Explorer

Live demo · API reference · Data schema

Reads: Labs and vitals

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Labs and vitals
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`baseline_col`	optional	No default	—	Labs and vitals
`visit_col`	optional	`VISIT`	Visit	Labs and vitals
`visitn_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`studyday_col`	optional	`DY`	Study day	Labs and vitals
`arm_col`	optional	`ARM`	Treatment arm	Labs and vitals

Participant Profile

Live demo · API reference · Data schema

Reads: Labs and vitals
Also reads, when supplied: Adverse events

Adverse events are optional: when supplied, the profile adds their summary and timeline on the labs study-day axis, reading the same columns the adverse-event charts do.

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Labs and vitals
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`normal_col_high`	required	`STNRHI`	Upper limit of normal	Labs and vitals
`normal_col_low`	optional	`STNRLO`	Lower limit of normal	Labs and vitals
`studyday_col`	optional	`DY`	Study day	Labs and vitals
`visit_col`	optional	`VISIT`	Visit	Labs and vitals
`visitn_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`baseline_col`	optional	No default	—	Labs and vitals
`p_alt_col`	optional	No default	—	Labs and vitals

QT Safety Explorer

Live demo · API reference · Data schema

Reads: ECG

Setting	Required	Default column	What it holds	Read from
`id_col`	optional	`USUBJID`	Participant	ECG
`measure_col`	required	`TEST`	Measure	ECG
`value_col`	required	`STRESN`	Result	ECG
`baseline_col`	required	`BASE`	Baseline value	ECG
`change_col`	optional	`CHG`	Change from baseline	ECG
`unit_col`	optional	`STRESU`	Unit	ECG
`arm_col`	required	`ARM`	Treatment arm	ECG
`visit_col`	optional	`VISIT`	Visit	ECG
`visitn_col`	optional	`VISITNUM`	Visit order	ECG
`baseline_flag_col`	optional	`ABLFL`	Baseline flag	ECG

Adverse Event Explorer

Live demo · API reference · Data schema

Reads: Adverse events

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Adverse events
`major_col`	required	`AEBODSYS`	Body system	Adverse events
`minor_col`	required	`AEDECOD`	Preferred term	Adverse events
`group_col`	required	`ARM`	Treatment arm	Adverse events
`placeholder_flag.value_col`	optional	No default	—	Adverse events

Adverse Event Timelines

Live demo · API reference · Data schema

Reads: Adverse events

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Adverse events
`seq_col`	required	`AESEQ`	Sequence	Adverse events
`stdy_col`	required	`ASTDY`	Start day	Adverse events
`endy_col`	required	`AENDY`	End day	Adverse events
`term_col`	required	`AETERM`	Reported term	Adverse events
`color.value_col`	required	`AESEV`	Severity	Adverse events
`highlight.value_col`	optional	`AESER`	Serious	Adverse events

Time-to-Event Explorer

Live demo · API reference · Data schema

Reads: Adverse events, Subject-level

Takes two tables: the adverse events as the events, without the placeholder rows for event-free participants, and the subject-level table as the population. The participant column must carry the same name in both.

Setting	Required	Default column	What it holds	Read from
`id_col`	optional	`USUBJID`	Participant	Adverse events, Subject-level
`group_col`	optional	`ARM`	Treatment arm	Subject-level
`fu_day_col`	optional	`EOSDY`	End-of-study day	Subject-level
`censor_desc_col`	optional	`EOSSTT`	End-of-study status	Subject-level
`event_day_col`	optional	`ASTDY`	Start day	Adverse events
`event_desc_col`	optional	`AEDECOD`	Preferred term	Adverse events

Biomarkers, from bio.viz

4 charts from bio.viz, a second chart library the demo app carries beside these and lists in a tab of its own. They read the standard domains through the same mapping, so a study mapped for the safety charts is mapped for them. Each links to its demo and its reference on bio.viz's site.

Group comparison

Live demo · API reference

Takes the tables: results from Labs and vitals; participants from Subject-level, when supplied
Reads: Labs and vitals
Also reads, when supplied: Subject-level

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Labs and vitals
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`visit_col`	required	`VISIT`	Visit	Labs and vitals
`visit_order_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`participant_id_col`	optional	`USUBJID`	Participant	Subject-level
`studyday_col`	optional	No default	—	Labs and vitals
`normal_col_high`	optional	No default	—	Labs and vitals
`normal_col_low`	optional	No default	—	Labs and vitals

Association scatter

Live demo · API reference

Takes the tables: results from Labs and vitals; participants from Subject-level, when supplied
Reads: Labs and vitals
Also reads, when supplied: Subject-level

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Labs and vitals
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`visit_col`	required	`VISIT`	Visit	Labs and vitals
`visit_order_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`participant_id_col`	optional	`USUBJID`	Participant	Subject-level
`studyday_col`	optional	No default	—	Labs and vitals
`normal_col_high`	optional	No default	—	Labs and vitals
`normal_col_low`	optional	No default	—	Labs and vitals

Correlation matrix

Live demo · API reference

Takes the tables: results from Labs and vitals; participants from Subject-level, when supplied
Reads: Labs and vitals
Also reads, when supplied: Subject-level

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Labs and vitals
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`visit_col`	required	`VISIT`	Visit	Labs and vitals
`visit_order_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`participant_id_col`	optional	`USUBJID`	Participant	Subject-level

Biomarker screen

Live demo · API reference

Takes the tables: results from Labs and vitals; participants from Subject-level, when supplied
Reads: Labs and vitals
Also reads, when supplied: Subject-level

Setting	Required	Default column	What it holds	Read from
`id_col`	required	`USUBJID`	Participant	Labs and vitals
`measure_col`	required	`TEST`	Measure	Labs and vitals
`value_col`	required	`STRESN`	Result	Labs and vitals
`visit_col`	required	`VISIT`	Visit	Labs and vitals
`visit_order_col`	optional	`VISITNUM`	Visit order	Labs and vitals
`unit_col`	optional	`STRESU`	Unit	Labs and vitals
`participant_id_col`	optional	`USUBJID`	Participant	Subject-level

The manifest's format

The manifest is written in format version 2. Version 2 lets a second chart library publish its own chart list in the same format, so the demo app can list its charts beside these, read from the same files through the same mapping. A library's chart list may leave out the domains: its charts read this standard set. The charts on this page use none of the fields version 2 adds, and each means what it meant in version 1. What a chart entry can say besides its domains and settings:

library names the chart library the chart comes from. Left out, it is safety.viz.
group names the group the chart is listed under: a standard domain, or one of the manifest's groups, each with the label on its tab and an order among such groups, which come after the domains. Left out, a chart is listed under the first domain it reads.
tables names the tables the chart's init takes when it takes several, each read from one standard domain and marked required or not. The chart is handed an object of those tables built from the loaded files, and an optional table with no file is left out of it.
unmappedSettings says what the chart is handed for a setting with nothing mapped: "null", no column, as when it is left out; or "omit", nothing at all, for a chart that refuses a null column setting.

Standard domain set

Subject-level subject

Adverse events ae

Labs and vitals bds

ECG eg

What each chart needs

Safety Histogram

Safety Outlier Explorer

Safety Results Over Time

Safety Shift Plot

Safety Delta-Delta

Hepatic Safety Explorer

Hepatic ALT Waterfall

Nephrotoxicity Explorer

Participant Profile

QT Safety Explorer

Adverse Event Explorer

Adverse Event Timelines

Time-to-Event Explorer

Biomarkers, from bio.viz

Group comparison

Association scatter

Correlation matrix

Biomarker screen

The manifest's format

Subject-level `subject`

Adverse events `ae`

Labs and vitals `bds`

ECG `eg`