Changelog

§ v1.15.0 (2022-03-22)

  • Use R9 data for all phenotype analyses.
  • Add information about specific control definitions to endpoint explainer.

Data v2022-03-22

FinnGen dataset R9.1.0
Intermediate case counts R9.1.0, using all FinnGen individuals, even those without genotype
Mortality R9.1.0, using core endpoints only
Cumulative incidence R9.1.0, using core endpoints only
Survival analyses R9.1.0, using endpoint priority list and core endpoints (175k endpoint pairs)
Drug statistics R9.1.0, using core endpoints only
Ontology v2020-08-10

§ v1.14.0 (2021-11-30)

  • 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

Finngen Data Freeze 8v4 - QCed, first-event
Endpoint survival analyses R8v4: survival analyses on endpoint pairs (226k) using endpoint priority list, with lagged hazard ratios.
Endpoints Endpoint definitions R8v4
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv
Correlations Phenotype R8v4, Genotype R8v4

§ v1.13.0 (2021-04-26)

  • Use R7 data for all phenotype analyses

Data v2021-04-23

Finngen Data Freeze 7v4 - QCed, first-event
Endpoint survival analyses R7v4: all survival analyses of endpoint pairs (> 3.8 millions) with lagged hazard ratios.
Endpoints Endpoint definitions R7v2
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv
Correlations Phenotype R7v4, Genotype R6

§ v1.12.0 (2021-04-12)

  • 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

Finngen Data Freeze 6 - QCed, first-event, filtered to match PheWeb data
Endpoint survival analyses v3-r6: all survival analyses of endpoint pairs (> 4.6 millions) with lagged hazard ratios.
Endpoints finngen_R6_v2_endpoint_definitions
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv
Correlations Phenotype R6v2, Genotype R6

§ v1.11.0 (2021-01-18)

  • 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

Finngen Data Freeze 6 - QCed, first-event, filtered to match PheWeb data
Endpoint survival analyses v3-r6: all survival analyses of endpoint pairs (> 4.6 millions) with lagged hazard ratios.
Endpoints finngen_R6_v2_endpoint_definitions
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv

§ v1.10.0 (2020-10-14)

  • FinnGen data freeze 6 dataset
  • Mortality statistics

Data v2020-10-14

Finngen Data Freeze 6 - QCed, first-event, filtered to match PheWeb data
Endpoint survival analyses v3-r6: all survival analyses of endpoint pairs (> 4.6 millions) with lagged hazard ratios.
Endpoints finngen_R6_v2_endpoint_definitions
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv

§ v1.9.0 (2020-07-14)

  • Responsive design to support mobile view.

Data v2020-04-28

Finngen Data Freeze 5 - QCed, longitudinal + first-event, filtered to match PheWeb data
Endpoint survival analyses v2-r5: all survival analyses of endpoint pairs (> 5 millions) with lagged hazard ratios.
Endpoints finngen_R5_v2_endpoint_definitions
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv

Source code

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

§ v1.8.3 (2020-06-30)

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

Data v2020-04-28

Finngen Data Freeze 5 - QCed, longitudinal + first-event, filtered to match PheWeb data
Endpoint survival analyses v2-r5: all survival analyses of endpoint pairs (> 5 millions) with lagged hazard ratios.
Endpoints finngen_R5_v2_endpoint_definitions
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv

Source code

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

§ v1.8.2 (2020-05-28)

  • Add interactions to drug statistics table.

Data v2020-04-28

Finngen Data Freeze 5 - QCed, longitudinal + first-event, filtered to match PheWeb data
Endpoint survival analyses v2-r5: all survival analyses of endpoint pairs (> 5 millions) with lagged hazard ratios.
Endpoints finngen_R5_v2_endpoint_definitions
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv

Source code

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

§ v1.8.1 (2020-05-26)

  • Add comparable box plots in survival analysis table.

Data v2020-04-28

Finngen Data Freeze 5 - QCed, longitudinal + first-event, filtered to match PheWeb data
Endpoint survival analyses v2-r5: all survival analyses of endpoint pairs (> 5 millions) with lagged hazard ratios.
Endpoints finngen_R5_v2_endpoint_definitions
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv

Source code

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

§ v1.8.0 (2020-04-28)

  • 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

Finngen Data Freeze 5 - QCed, longitudinal + first-event, filtered to match PheWeb data
Endpoint survival analyses v2-r5: all survival analyses of endpoint pairs (> 5 millions) with lagged hazard ratios.
Endpoints finngen_R5_v2_endpoint_definitions
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv
Heritability removed

Source code

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

§ v1.7.1 (2020-01-22)

Source code

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

Data v2020-01-22

Finngen Release 4 - QCed, longitudinal + first-event, filtered to match PheWeb data
Risteys endpoint associations v2-r4: all associations of endpoint pairs (> 4.7 million associations) with lagged hazard ratios.
Endpoints finngen_R4_endpoint_definition
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID all_matching_FG_DOID_MESH_excl.csv
Heritability h2_results
  • 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.

§ v1.7.0 (2019-12-19)

Source code

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

Data v2019-12-19

Finngen Release 4 - QCed, longitudinal + first-event, filtered to match PheWeb data
Risteys endpoint associations v2-r4: all associations of endpoint pairs (> 4.7 million associations) with lagged hazard ratios.
Endpoints finngen_R4_endpoint_definition
Ontology EFO 2019-12-15 EFO 3.13.0
Ontology DOID R4_ontology_mapping
Heritability h2_results
  • 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.

§ v1.6.0 (2019-11-04)

Source code

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

Data v2019-11-04

Finngen Release 4 - QCed, longitudinal + first-event, filtered to match PheWeb data
Risteys endpoint associations v1-r4 all demo endpoints (113k associations)
Endpoints finngen_R4_endpoint_definition
Ontology EFO 2019-06-17 EFO 3.7.0
Ontology DOID endpoint_doid_exact_names_ag_stop_words_syno_250619
  • 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.

§ v1.5.2 (2019-10-09)

Source code

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

Data v2019-10-09

Finngen Release 3 - QCed, longitudinal + first-event, filtered to match PheWeb data
Risteys endpoint associations v1-r3 all demo endpoints (86k associations)
Endpoints Endpoint_definitions_FINNGEN_ENDPOINTS_DF3_V1
Ontology EFO 2019-06-17 EFO 3.7.0
Ontology DOID endpoint_doid_exact_names_ag_stop_words_syno_250619
  • Add a QC step to the pipeline.

§ v1.5.1 (2019-09-20)

Source code

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

Data v2019-09-20

Finngen Release 3, longitudinal + first-event, filtered to match PheWeb data
Risteys endpoint associations v1-r3 all demo endpoints (86k associations)
Endpoints Endpoint_definitions_FINNGEN_ENDPOINTS_DF3_V1
Ontology EFO 2019-06-17 EFO 3.7.0
Ontology DOID endpoint_doid_exact_names_ag_stop_words_syno_250619
  • 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.

§ v1.5.0 (2019-09-05)

Source code

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

Data v2019-09-04

Finngen Release 3, longitudinal + first-event, filtered to match PheWeb data
Risteys endpoint associations v1b-r3 partial demo endpoints (83k associations)
Endpoints Endpoint_definitions_FINNGEN_ENDPOINTS_DF3_V1
Ontology EFO 2019-06-17 EFO 3.7.0
Ontology DOID endpoint_doid_exact_names_ag_stop_words_syno_250619

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.

§ v1.4.0 (2019-07-29)

Source code

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

Data v2019-07-29

Finngen Release 3, longitudinal, filtered to match PheWeb data
Endpoints Endpoint_definitions_FINNGEN_ENDPOINTS_DF3_V1
Ontology EFO 2019-06-17 EFO 3.7.0
Ontology DOID endpoint_doid_exact_names_ag_stop_words_syno_250619
  • Use a 30 day time-window to merge events, more information on the Documentation page.

§ v1.3.0 (2019-07-08)

Source code

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

Data v2019-07-08

Finngen Release 3, longitudinal, filtered to match PheWeb data
Endpoints Endpoint_definitions_FINNGEN_ENDPOINTS_DF3_V1
Ontology EFO 2019-06-17 EFO 3.7.0
Ontology DOID endpoint_doid_exact_names_ag_stop_words_syno_250619
  • 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.

§ v1.2.0 (2019-06-26)

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.

Finngen Release 3, longitudinal
Endpoints Endpoint_definitions_FINNGEN_ENDPOINTS_DF3_V1
Ontology EFO 2019-06-17 EFO 3.7.0
Ontology DOID endpoint_doid_exact_names_ag_stop_words_syno_250619

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.

§ v1.1.1 (2019-06-04)

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.

§ v1.1.0 (2019-06-03)

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.

§ v1.0.1 (2019-05-23)

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.

§ v1.0.0 (2019-05-14)

Source code

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

Data v2019-05-10

Finngen Release 3
Endpoints DF3_FINAL_witdpw_2019-02-27
Ontology DOID 2019-04-18
Ontology XREFs 2019-04-18

Notes

First release.

Features

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