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Webinterface

Open beta.pk-db.com to explore PK-DB in your browser. No installation is needed. Public study browsing is available without an account; downloads and access to shared private studies require sign-in.

The screenshots below show the current frontend with artificial demonstration data. Study names, counts, and values illustrate the interface, not scientific results from the public collection. Select a screenshot to view it at full size. They are rendered from the disposable website of the browser tests, see Isolated frontend browser checks.

For a scientific example of how a publication is represented in PK-DB, see the example study.

Explore database coverage

The landing page shows current totals and interactive charts for studies, substances with timecourses, and PK parameter values. Choose a year range, switch studies and substances between annual and cumulative counts, or select a PK parameter to compare reported and calculated values. The substance chart ranks current timecourse coverage.

Hover for values, drag to zoom, and double-click to reset. Each chart includes a data table and a PNG download. Counts reflect studies you can access and refresh when your session changes. Years use the study date; undated studies appear in current totals and a separate notice. Cumulative substance counts include each substance only once. These charts describe the current collection by study date, not earlier database snapshots.

Browse studies

Open Studies in the main navigation to list the studies that you may read. Each row shows the identity of a study, <substance>/<name>, with the title of its publication, the PKDB identifier of its release, and its curators. Select a study to open its study page.

The Studies page as a visitor sees it: Search studies, the Substance and Curator filters, and three public studies with their release and their curator.

Search studies matches the identity and the title. Substance shows the studies of one substance, also those whose interventions or data name it. Curator shows the studies of one curator; when you are signed in, it offers you first as Me. Select a column header to sort by it. The Studies page lists the study format 2 studies that have a study page; find the other studies with the data search below.

When you are signed in and may curate one of the listed studies, the list also shows the columns Issue (the GitHub issue of the study), Review (Draft, In review or Approved), Open items (the open review items) and Problems (the warnings of the last upload, or valid), and the status chips All, Needs attention, Draft, In review and Approved. These columns are filled for the studies you may curate and show - for the others. See What each reader sees.

The Studies page as the curator of four studies sees it: the status chips beside the filters, and the columns Issue, Review, Open items and Problems, with two warnings for caffeine/Demo2020.

Find studies

Open Explore data to reach Search pharmacokinetic data. The research filters appear on the left on a desktop; on a smaller screen, open Filters and Search.

Study search showing research filters, applied selection, result categories, and four study rows

  1. Choose the substances, measurement types, subject characteristics, or study criteria relevant to your question.
  2. Select the subject types, licences, and measurement types you want to include.
  3. Choose Search to apply the filters. Editing a filter changes the draft; it does not change the results until you search.
  4. Review the applied selection and the counts beside each result category.

The example searches load a draft you can inspect and adjust before choosing Search. If no results match, broaden the filters and search again.

Matching measurements and related records selects measurements matching the constraints and returns their associated study, subject, and intervention context. Related records may contain information beyond the individual match.

All data from qualifying studies returns the broader study context. Different records within one study can satisfy different conditions, so not every returned measurement necessarily matches every filter.

Use Share applied search to copy the current search link. The link preserves criteria; it does not freeze the data or grant another person access to private studies.

Switch between Studies, Groups, Individuals, Interventions, Measurements, Timecourses, and Scatter data to explore the same applied selection from different perspectives.

Measurements tab showing values, units, and related study information

Read the measurement type, substance, unit and Value together. The Value column shows one value per row: the arithmetic mean, else the median, else the geometric mean, followed by its spread (± SD, ± SE or the coefficient of variation in percent, and for a geometric mean ×/÷ GSD or the geometric coefficient of variation) and the range when minimum and maximum are reported. A dash marks every empty cell. Statistics and times are shown with four significant digits and the stored values are unchanged, and the value of a single subject or of a summary whose statistic the publication does not state appears as a plain number. Interventions show their dosing schedule as a list of times (0, 12, 40 h) or as a regular schedule (every 24 h, 7 doses from 0 h). Open a record to inspect its subject and intervention context before comparing values across studies.

Search table refines only the current table; choose Apply table search to apply it. It does not replace the research filters. Use column sorting and Previous / Next to navigate longer result sets. The Value column sorts by the same mean, median or geometric mean that it shows, and rows without a value come last.

Open a study

Select a study on the Studies page or in the results of the data search to open it. A study opens at /data/<substance>/<name>, for example /data/caffeine/Harder1988. Links by the PKDB identifier of a released study, such as /data/PKDB00198, or by the former study format 1 identifier of a migrated study, such as /data/Vilsboll2008, keep working and lead to the same page, also after the study is renamed. To find a study by its PKDB identifier, search for it or use the PKDB identifiers filter.

The study page

A study format 2 study opens on its study page. It shows the study with the same views as the local curation app, read-only. The header shows the identity of the study, its release, the title of its publication, and its PMID. The tabs Metadata and Data switch between the sections; the address of a section ends with its name, such as /data/<substance>/<name>/data.

The Metadata section of a study page as a visitor sees it: the cards Reference, People, Access and provenance, Release, and Descriptions and comments.

Metadata shows the reference, the creator, curators and collaborators, the licence, the access, the provenance, the release, and the descriptions and comments of the study.

The Data section of a study page as a visitor sees it: the navigator with the tables grouped by their information and the sources, the plot of the rows mapped from the figure Fig1 with its two series, and the rows of timecourses_Fig1.tsv.

Data shows the tables of the study and the sources of the publication that they come from, such as a figure, a table or the text. The navigator on the left groups the tables by their information: subjects, interventions and data. Choose a table to see its rows, and a source to see the plot of the rows mapped from it; select a point to select its row. Hide empty columns hides the columns without a value. Whether a reader also sees the images of the sources, the raw extractions and the paper depends on what they may do, see the next section.

All studies goes back to the Studies page as you left it. When the data search opened the study, Back to the search goes back to the search where you left it.

What each reader sees

The website shows the curation of a study only to who may change the study: its assigned curators, the reviewers of a public study, and administrators. Everyone else sees the public view.

Reader Studies Study page
Visitor, not signed in The public studies, with the columns Study, Release and Curators. Metadata and Data: the tables and the plots of their mapped rows, without images of the sources, raw extractions or the paper.
Signed in, without rights on the study As a visitor. As a visitor. A private study answers Not found.
Assigned curator of the study, or reviewer of a public study Also the private studies they curate, and the columns and status chips of the curation. The curation view: the issue, the review status and the problems in the header, and the tabs Problems and Review with their counts. Data also shows the paper, the images of the sources with their digitization, and the raw extractions.
Administrator Every study, with the columns of the curation for each. The curation view of every study.

The Data section of a study page as its curator sees it: the issue, the review status and the two warnings in the header, the tabs Problems and Review, the raw extraction and the paper in the navigator, the digitization of the figure Fig1 on its image with its warning, and the rows of timecourses_Fig1.tsv.

Problems lists the warnings of the validation of the last upload, with the acknowledgements of review.json; they change with the next upload. Review lists the review items with their threads and the rows that they target, and filters them by status and kind. The study page does not edit a study: change it with the local curation app and upload it again.

The Review section of a study page as its curator sees it: all four review items, and the resolved issue about the number of subjects with its reply and the row of subjects.tsv that it targets.

The record page

A study format 1 study, and a study format 2 study that was uploaded before the website had study pages, opens on its record page; a study format 2 study gets its study page when it is uploaded again. A status strip at the top of the record page shows the Identifier, the PKDB identifier and the Released date of the study. Who may curate the study also sees its Curation issue (a link to the issue on GitHub) and its Review status (draft, in review or approved) with the number of open review items. Entries that a study does not have are left out. Under Explore all data from this study, choose a Study data category to browse its groups, individuals, interventions, measurements, or series.

The record page of a study format 1 study: its identifier, its reference and data source, and the study data category selector above the records of the study

Related-record buttons let you follow links between a measurement, its subject, and its intervention. Back to previous record retraces that exploration; Close details returns to the search. Study details can include records outside your applied search because they show the study's broader context.

Explore timecourses and scatter data

On a record page, open a timecourse record and choose Show timecourse plot, or open a scatter record and choose Show scatter plot. The Data section of a study page plots the rows mapped from a source directly. Inspect axis labels and units, and use Accessible plot data and uncertainty to read the values as a table.

Timecourse detail with a plot and controls for inspecting its values

A plot shows the complete subset as context, including points that may not individually match your search. A logarithmic axis cannot display zero or negative values; check the accompanying table when these are relevant.

Sign in and download

Open Account to sign in with your username and password. If you need an account or an API key, follow Accounts and API keys.

Login form with account creation and password recovery links

Study attachments are listed on the record page of a study when available to your account. Sign in before opening or downloading them. On a study page, the curators of the study see its paper and images in the Data section. For a reproducible dataset download with explicit filters, use the Python client or REST API.

Review the study licence and cite the underlying publication and PK-DB when using the data.