Study format¶

A study folder in study format 2 contains study.json, reference.json, review.json, the tab-separated tables below, the publication PDF and an image <study>_<source>.png for every paper table or figure the data come from. pkdb format writes all files in canonical form, pkdb validate checks them, and pkdb schema export writes the same definitions as JSON Schema.

Identity and upload¶

A study is identified by its folder location <substance>/<name>, for example caffeine/Harder1988: the folder name is the study name and its parent folder the substance. The folder names publication and validate are reserved, because PK-DB uses them in study URLs. pkdb upload sends the exact text of study.json and reference.json and every other file of the folder to /api/v2/studies/<substance>/<name>, where the server validates the folder like pkdb validate and stores the study. The study page is /data/<substance>/<name>.

A released study has a PKDB identifier in the release block of study.json. Uploading a folder with a release.pkdb_id takes over the study that PK-DB stores under that identifier and renames it to the folder location, so a moved or renamed folder keeps its study. A folder without one, or whose PKDB identifier no stored study has, takes over the study format 1 study of the same publication and source, if you may edit it. PKDB identifiers and former study format 1 identifiers in URLs, such as /data/PKDB00198 or /data/Vilsboll2008, redirect to the study.

Statistics and schedules¶

There is no value column. mean is the arithmetic mean, the value of a single subject (count 1) or, with the calculation unspecified summary, the central value of a summary whose statistic the publication does not state. cv and gcv are entered in percent and are fractions in the prepared study and the API. A digitized error_bar with its error_type completes sd, se or gsd; missing sd, se and cv are derived from each other, and gsd and gcv as well, where the reported values allow it, and reported statistics that contradict each other, including an error bar, are a warning that a review item acknowledges at the column of the statistic that disagrees with the most others (see the data model). An intervention time is a number, or a ;-separated list for an irregular schedule; a regular schedule uses interval and doses instead.

Tables¶

TSV encoding¶

• UTF-8 without byte order mark, LF line endings and a final newline.
• Tab separated without quoting. Cells contain no tabs or line breaks.
• One header row with every template column in template order.
• An empty cell means missing. NR (not reported) is allowed only in time and time_unit and their scatter variants x_time, x_time_unit, y_time and y_time_unit.
• Numbers use a decimal point and are written in their shortest form.
• pkdb format sorts the rows and writes the study column and, in files named after a source, the source column.

subjects.tsv¶

Groups and individuals. A subject with count 1 is an individual; every subject except all has a parent group.

interventions.tsv¶

Interventions such as doses, fasting or smoking, referenced by name from the other tables.

characteristica.tsv¶

Baseline values of subjects, such as age, weight, sex or creatinine clearance.

outputs_<source>.tsv¶

Single values after interventions, such as pharmacokinetic parameters, from one paper table or figure.

timecourses_<source>.tsv¶

Timecourse points from one paper figure or table. Rows with the same label form one series.

scatters_<source>.tsv¶

Points of scatter plots, one row per point with an x and a y value.