Changelog

§ 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 phenocode 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 phenocode 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 phenocodes.
  • Associations: added lagged hazard ratios.
  • Ontology: improved matching of FinnGen phenocodes to DOID, MeSH, etc.
  • Heritability: added SNP-h2 liability statistics for some phenocodes.

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 phenocodes (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 phenocode 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 phenocodes (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 phenocodes (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 phenocodes (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 phenocodes 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 Methods 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 phenocodes 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 phenocode name on the page title: following a feedback from a Risteys user, added the phenocode name on the page as this is what leads users from the search box the phenocode 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