Technical notes

This page summarises the key technical revisions made to platform code to improve and streamline the full stack code in line with major releases scheduled to incorporate new data and features.

20.09

Open Targets Platform 20.09 was released on Thursday 24 October 2020.

Release synchronised with:

  • EFO 3.21 (August 2020)

  • Ensembl release e!100 (April 2020)

Updated docker images:

Pipeline configuration file:

Release highlights:

Technical release information:

Data team

Release details:

New features / updates / bug fixes:

  • Add allelic requirement, mutation consequence and disease confidence to G2P evidence strings #1147

  • Use target-disease evidence from ClinGen #1180

  • Include all Gene2Phenotype gene panels in evidence #1078

  • Score G2P evidence based on disease confidence #1148

  • Review of UniProt evidence strings #709, #1141, #1135

  • Review mapping of Gene2Phenotype traits to EFO #980

Back-End / Infrastructure

Configuration notes:

  • ElasticSearch 7.7.0

  • Data pipeline image for Python 3.6

  • Google Cloud Platform configuration to run pipeline

    • CPU = 16

    • RAM = 480GB

New features / updates / bug fixes:

  • Update data pipeline for ClinGen #1181

Front-End

  • Add ClinGen to association page facets #1188

  • Include link to Open Targets COVID-19 target prioritisation tool #1150

  • Generate XML sitemaps for 20.09 release #1187

  • Update links on Data Downloads page for 20.09 #1189

  • Update text on /variants page #1198

20.06

Open Targets Platform 20.06 was released on Tuesday 16 June 2020.

Release synchronised with:

  • EFO 3.18 (May 2020)

  • Ensembl release e!100 (April 2020)

Updated docker images:

Pipeline configuration file:

https://storage.cloud.google.com/open-targets-data-releases/20.06/input/mrtarget.data.20.06.yml

Release highlights:

Technical release information:

Data team

Release details:

New features / updates / bug fixes:

  • Updated CHEMBL ID to DrugBank ID mapping file #1085

  • Apply filter to Locus2Gene data from Open Targets Genetics Portal #1050

  • Expression Atlas and PheWAS Catalog unique association fields misspecified #795

  • Expression widget empty for ADORA3 #127

  • Review EFO mapping of Gene2Phenotype diseases #1077

  • JSON schema not stringent with date format #1090

  • EVA evidence fixes #843

Back-End / Infrastructure

Configuration notes:

  • Elasticsearch 7.7

  • Data pipeline image for Python 3.6

  • Google Cloud Platform configuration to run pipeline

    • CPU = 16

    • RAM = 480GB

New features / updates / bug fixes:

  • Update LINK dictionaries #1051

  • Rerun LINK to capture publications to June 2020 #1052

Front-End

  • Create link to profile pages in rewrite #1086

  • Update links on downloads page #1006

  • Update links in Platform footer #1031

  • Generate XML sitemaps #1048

  • Netlify deploy configuration updates #984

20.04

Open Targets Platform 20.04 was released on Monday 27 April 2020.

Release synchronised with:

  • EFO 3.16 (March 2020)

  • Ensembl 99 (January 2020)

Updated docker images:

Pipeline configuration file:

Release highlights:

‌Technical release information:

Data Team

Release details:

New features / updates / bug fixes:

  • Review COSMIC evidence and integrate new Hallmarks of Cancer annotation file (v91) #811, #951

  • Fix invalid intOGen evidence strings #853

  • Update Gene2Phenotype data #931, #951

  • Update PheWAS data #824, #874, #420, #951

  • Update PhenoDigm #951

  • Fixes to Open Targets Genetics Portal evidence strings #876 #857

  • Fixes to missing “evidence_codes_info” in Genetics Portal and PheWAS evidence #873, #856, #874, #757

  • Fix EFO mapping in EVA #893, #104, #841, #843

  • Rescue “cardiovascular disease” therapeutic area in EFO slim #892

  • Fix to remove duplicates in expression atlas evidence #795, #951

  • Updated chemical probes #951

Back-End / Infrastructure

Configuration notes:

  • ElasticSearch 7.6.1

  • Data pipeline image for Python 3.6

  • Google Cloud Platform configuration to run pipeline

    • CPU = 16

    • RAM = 480GB

New features / updates:

  • Integrate new tractability data #880 and update API gene index response #881

  • Integrate new experimental toxicity safety data #904 and update API gene index response #905

  • Updates to platform-input-support scripts #952, #953, #845

  • Make tractability, safety, and baseline expression data files available for download #926

Front-End

New features:

  • Display tractability assessment for other clinical modalities and link to /downloads/data page #882

  • Create data table for experimental toxicity data within the Target Safety tab #906

  • Add links to tractability, safety, and baseline expression files on downloads/data page #942

  • Update Somatic Mutations data table based on changes to COSMIC #939

Bug fixes:

  • Hide Cancer Hallmarks data table when no hallmarks data is available #947

  • Update Platform homepage and footer #954

  • Fix tooltip overflow issue #946

  • Round L2G score in Genetic Associations data table #965

Other / maintenance:

  • Generate XML sitemaps #978

  • Netlify configuration updates #984

20.02

Open Targets Platform 20.02 was released on Monday 2 March 2020.

Release synchronised with:

  • EFO 3.14 (January 2020)

  • Ensembl 98 (September 2019)

Updated docker images:

Pipeline configuration file:

Release highlights:

‌Technical release information:

Infrastructure

  • Update JSON schema to 1.6.4

  • Fixed uploading of normal tissue file for platform-input-support scripts #776

  • Fixed ES7 Docker image connection issue #736

Data / Back-End

  • CHEMBL: updated evidence strings using CHEMBL26 data #835, updated drug index #834; ran adverse events pipeline with new drugs #833

  • intOGen: updated evidence strings using latest intOGen release #813

  • Changes in somatic mutation evidence normalization #811

  • Updated CHEMBL-DrugBank ID mapping file #802

  • Fixed GWAS evidence strings with a score of 0 #434

  • GWAS evidences are now sourced from Open Targets Genetics portal instead of GWAS Catalog directly #815

  • Fixed UniProt-Ensembl mapping issue #801

Front-End

  • Fix to external links in RNA Expression data table on evidence page #812

  • Added new TEP - MTHFR #458

  • Updates to Somatic Mutation data table on evidence page #840

  • Updates to Genetic Association data table on evidence page #816

  • Association page facets updated to allow users to filter by Open Targets Genetics Portal evidence #849

19.11

19.11 was released on Thursday 28 November 2019

Release synchronised with:

  • EFO 3.11 (October 2019)

  • Ensembl 98 (September 2019)

Updated docker images:

Pipeline configuration file:

Release highlights:

Technical release information:

  • Infrastructure:

    • Python 3 migration

      • Now running in Python 3: data-pipeline (Note: we expect the pipeline to continue to run with Python 2 but we will no longer support the pipeline in Python 2 as it has reached its end-of-life)

      • Running a mix of Python 2 and 3: client, validator and ontologyutils

      • Still running in Python 2 only: Open Targets REST API and Open Targets LIterature coNcept Knowledgebase (LINK)

  • Pipeline:

  • REST API:

    • Add DrugBank ID - #612

    • Return clinical trial IDs in array - #686

    • Add canonical SMILES for a drug - #704

    • Add URLs to mechanism_of_action data - #687

    • Add adverse events data - #739

    • Change to how EFO3 descriptions appear in API response - #756

  • Front-end webapp:

    • Include new visualisation for adverse events data - #741

    • Display more details in drugs data tables - #730

    • Fix bubbles and tree visualisations (EFO3) - #183

    • Fix disease classification visualisation (EFO3) - #457

    • Show DrugBank ID and link on drug profile page - #703

    • Bug fixes: #782, #781, #780, #734, #766, #783

  • Other:

    • LINK: review Python dependencies - #769

    • LINK: update dictionaries - #770

    • LINK: rerun pipeline with EFO3 - #750

19.09

Release synchronised with:

EFO 2.106 (March 2019 - final release of Version 2)

Ensembl 97 (July 2019)

Updated docker images:

Pipeline configuration file:

Release highlights:

Blog: http://blog.opentargets.org/2019/09/24/open-targets-platform-release-19-09-is-out/

Release notes: https://docs.targetvalidation.org/release-notes

Technical release information:

19.06

Release synchronised with:

EFO 2.106 (March 2019 - final release of Version 2)

Ensembl 96 (Apr 2019)

Updated docker images:

Pipeline configuration file:

Release highlights:

Blog: http://blog.opentargets.org/2019/06/28/open-targets-platform-release-19-06-is-out

Release notes: https://docs.targetvalidation.org/release-notes

Technical release information:

19.04

Updated docker images:

Pipeline configuration file:

Release highlights:

Blog: http://blog.opentargets.org/2019/05/01/open-targets-platform-release-19-04-is-out/

Release notes: https://docs.targetvalidation.org/release-notes

Technical release information:

19.02

Updated docker images:

Technical release information: