• Create this FinRegistry-FinnGen Risteys version, which includes results also from FinRegistry project, in addition to FinnGen. Main changes to the portal are listed below.
• Use also FinRegistry data for main phenotype analyses: Key figures, Age distribution, Year distribution, and Cumulative incidence function
• Update analyses:
• Key figures show median age instead of mean age
• Cumulative incidence function (see the Documentation page for details)
• Add a new analysis: Mortality from FinRegistry data
• Add a new section: Relationships between endpoints, that shows case overlaps, Survival analysis results, Genetic correlations, and Genetic signals.
• Update ontology mapping
• Update user interface:
• Update homepage
• Update documentation
• Update layout and color scheme
• Update endpoint definition section
• Add links to all versions of FinnGen Risteys portals
• Use R10 data for all analyses.

Data v2021-10-31

Source code

Check the code for Risteys portal and pipeline for v2.0.0 on GitHub.

• Use R8 data for all phenotype analyses
• Add upset plots and detailed tables of case counts by code
• Show variant list when clicking on a coloc GWS hits in the correlation table (needs FinnGen authentication)

Data v2021-04-23

Source code

Check the code for Risteys portal and pipeline for v1.14.0 on GitHub.

• Use R7 data for all phenotype analyses

Data v2021-04-23

Source code

Check the code for Risteys portal and pipeline for v1.13.0 on GitHub.

• Add correlation table with phenotypic and genetic correlations across endpoints.
• Add Similar endpoints to navigate between FinnGen endpoints based on overlap of cases.
• Fix drug table disappearing on search in some special cases.

Data v2021-04-12

Source code

Check the code for Risteys portal and pipeline for v1.12.0 on GitHub.

• Add endpoint explainer table-diagram for the endpoint definition.
• Improve parsing of ICD-10 in enpoint definition.
• Add information on potential outpatient registry bump in 1998.
• Use binned hazard ratios for the distribution plots in the survival analysis table.

Data v2021-01-18

Source code

Check the code for Risteys portal and pipeline for v1.11.0 on GitHub.

• FinnGen data freeze 6 dataset
• Mortality statistics

Data v2020-10-14

Source code

Check the code for Risteys portal and pipeline for v1.10.0 on GitHub.

• Responsive design to support mobile view.

Data v2020-04-28

Source code

Check the code for Risteys portal and pipeline for v1.9.0 on GitHub.

• Add Download CSV button for survival analyses and drug statistics tables.
• Misc. fixes in tables.

Data v2020-04-28

Source code

Check the code for Risteys portal and pipeline for v1.8.3 on GitHub.

• Add interactions to drug statistics table.

Data v2020-04-28

Source code

Check the code for Risteys portal and pipeline for v1.8.2 on GitHub.

• Add comparable box plots in survival analysis table.

Data v2020-04-28

Source code

Check the code for Risteys portal and pipeline for v1.8.1 on GitHub.

• Now using FinnGen Data Freeze 5.
• Renamed association to survival analysis.
• Add drug statistics.
• Survival analysis plot: allow toggling of Y axis (p or HR).
• Updated pipeline for DF5 and performance.

Data v2020-04-28

Source code

Check the code for Risteys portal and pipeline for v1.8.0 on GitHub.

Source code

Check the code for Risteys portal and pipeline for v1.7.1 on GitHub.

Data v2020-01-22

• Ontology: increase accuracy for MESH

Misc

• Tables: replace N/A with - to improve readability.
• Data source: link ICD-10 codes to ICD-10 browser.
• Associations: show > 100 when HR is > 100
• Associations: change styling of the plot to differentiate before / after associations as well as using more opaque colors.
• Help panes: make it clearer that the data is example data and not real data.

Source code

Check the code for Risteys portal and pipeline for v1.7.0 on GitHub.

Data v2019-12-19

• Associations: QCed and computed all associations between pairs of FinnGen endpoints.
• Associations: added lagged hazard ratios.
• Ontology: improved matching of FinnGen endpoints to DOID, MeSH, etc.
• Heritability: added SNP-h² liability statistics for some endpoints.

Features

• Associations: show a message that association data is being loaded.

Source code

Check the code for Risteys portal and pipeline for v1.6.0 on GitHub.

Data v2019-11-04

• Use FinnGen R4 data.
• Associations: filter out overlapping endpoints (by ICD or hierarchy) when computing statistics.
• Associations: remove sex covariate for sex-specific endpoints.

Features

• Add a search bar on the endpoint pages.
• Use first-event data wherever it is more meaningful.
• Add help buttons in the statistics tables.
• Change the association table to be (hopefully) more readable.

Source code

Check the code for Risteys portal and pipeline for v1.5.2 on GitHub.

Data v2019-10-09

• Add a QC step to the pipeline.

Source code

Check the code for Risteys portal and pipeline for v1.5.1 on GitHub.

Data v2019-09-20

• All the demo endpoint associations are now present.

Features

• Show more information in the data source table.
• Clearly show which version of the data is used by displaying "R3" in the title.

Misc

• Remove the medication table for now, as it needs further data processing and QC.
• Display < 1e-100 for low p-values.

Source code

Check the code for Risteys portal and pipeline for v1.5.0 on GitHub.

Data v2019-09-04

Summary

Add association data with plot and table.

Features

• Add association plot.
• Add association table.
• Links to included endpoints in the data source information.

Fixes

• Fix the histogram sizes to not overflow the page width.

Source code

Check the code for Risteys portal and pipeline for v1.4.0 on GitHub.

Data v2019-07-29

• Use a 30 day time-window to merge events, more information on the Documentation page.

Source code

Check the code for Risteys portal and pipeline for v1.3.0 on GitHub.

Data v2019-07-08

• Use the same data as PheWeb for consistency accross FinnGen web tools.
• Filter out comorbidities.

Features

• Add demo endpoints on home page.
• More informative 404 page.

Fixes

• Remove endpoints without any statistics.
• Year distribution plot is now always toggable.
• Age brackets are now 0—9, 10—19, etc. instead of 0—10, 11—20, etc.
• Minor styling changes.

Source code

Check the code for Risteys portal and pipeline for v1.2.0 on GitHub.

Data v2019-06-26

Using a new pipeline to process and import the FinnGen data and ontology in Risteys.

Summary

FinnGen data on ontologies processed with a new pipeline. Usability changes thanks to user feedback.

Features

• New pipeline to process FinnGen data and ontology: the new pipeline uses the longitudinal data from FinnGen, results should not be different than before.
• Add endpoint name on the page title: following a feedback from a Risteys user, added the endpoint name on the page as this is what leads users from the search box the endpoint page.
• Change statistics table layout: following a feedback from a Risteys user, metrics are now as rows and sex as columns, leading to more readable tables.
• Add a toggle cumulative button for the year distribution plot.
• Add link to GitHub repository in the page header.
• Add a Methods page and a link to it in the page header.

Source code

Check the code for Risteys portal and pipeline for v1.1.1 on GitHub.

Data v2019-05-10

No change in the data source since v1.0.0.

Notes

Small styling changes.

Features

• Make the PheWeb link more visible.
• Year-distribution plot: rework how bins with individual-level data (<5 individuals) are handled. All the bins in the tails that have <5 individuals are not shown. Bins with <5 individuals inside the distribution are shown as if the value was 0 and the plot subtitle shows as bins with <5 individuals are not shown.

Source code

Check the code for Risteys portal and pipeline for v1.1.0 on GitHub.

Data v2019-05-10

No change in the data source since v1.0.0.

Notes

Mostly polishing / styling changes.

Features

• Endpoint plots: don't display the distribution tails if they have individual-level data (bins with individual-level data in the middle of the distribution are still shown as grey rectangles).
• Endpoint plots: angle the labels for the year distribution to improve readability.
• Improve page loading speed by minimizing and compressing assets.
• Search in the description of endpoints.
• Search by endpoint name.

Fixes

• Return a 404 error page when an endpoint is not found.
• Minor display improvements on the search page and the endpoint page.

Source code

Check the code for Risteys portal and pipeline for v1.0.1 on GitHub.

Data v2019-05-10

No change in the data source since v1.0.0.

Notes

Bug fix release.

Fixes

• Prevalence is now correct for all sex categories.

Source code

Check the code for Risteys portal and pipeline for v1.0.0 on GitHub.

Data v2019-05-10

Notes

First release.

Features

• search by endpoint name or ICD code
• get statistics for an endpoint: key figures, clinical metrics and distribution plots