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.

20.02

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: