25.03 Platform release now live! Open Targets Genetics data update

[hcornu]

We have just released the latest update to the Open Targets Platform — 25.03.

This release brings variant, study, and credible set information into the Open Targets Platform, effectively uniting the Open Targets Platform and Open Targets Genetics into a one-stop shop for human genetic and target discovery information.

This data release supersedes the last Open Targets Genetics release. Please note that we no longer maintain Open Targets Genetics, and the web interface will soon be deprecated. If you have concerns or comments about this, please let us know in the comments below.

The expanded Platform retains all of the existing data and functionalities, but now includes detailed information about disease-causing variants and their gene predictions based on our in-house Locus-to-Gene machine learning model, allowing you to better explore and connect genetic data. You can interpret gene-disease evidence from both common and rare variation in one interface, and in multiple ancestries.

Evidence metrics for this release:

This release integrates 28,168,992 evidence strings to build 10,162,821 target-disease associations between 28,327 diseases and 78,766 targets from the following 23 public resources:

• 3,138,383 genetic evidence from European Variation Archive (EVA)
• 1,082,677 GWAS credible sets from GWAS Catalog, FinnGen through Gentropy
• 4,181 genetic evidence from Gene2Phenotype
• 34,784 genetic evidence from the Genomics England PanelApp
• 3,016 genetic evidence from ClinGen
• 6,293 genetic evidence from Orphanet
• 36,805 genetic evidence from Gene burden
• 21,711 genetic evidence from CRISPRBrain
• 6,714 genetic evidence from UniProt Literature
• 9,719 somatic evidence from European Variation Archive (EVA)
• 4,224 somatic evidence from intOGen
• 82,754 somatic evidence from the Cancer Gene Census
• 33,047 somatic evidence from Uniprot
• 573,124 drug evidence from ChEMBL
• 229,404 expression evidence from Expression Atlas
• 10,162 affected pathway evidence from Reactome
• 72,406 affected pathway evidence from SLAPenrich
• 378 affected pathway evidence from PROGENy
• 390 systems biology evidence from SysBio
• 1,300 somatic evidence from the Cancer Genome Interpreter
• 517 CRISPR-Cas9 (Cancer Cell Lines) evidence from Pacini et al. (2024)
• 1,175,688 mouse model evidence from IMPC
• 21,641,315 scientific literature evidence from co-occurrence mining in Europe PMC

Additionally, the Platform now allows users to explore data on 18,081 drugs.

For more details and numbers, read the 25.03 blog post.

[alhenry]

Dear Open Targets team,

Thank you for the new release. Could you clarify whether all the data from previous Open Targets Genetics portal are now included in the Open Targets Platform?

When searching for a single variant on Open Targets Genetics web portal, the dashboard shows Variant summary, Assigned genes, PheWAS, Forest Plot, GWAS lead variants, and Tag variants. However, the variant-level dashboard on the new Open Targets Platform seems to show a different information.

Is there a way to retrieve the data from previous Open Targets Genetics portal through the new Open Targets Platform portal?

Many thanks,
Albert

[ochoa]

Dear Albert,

The new data included in the Platform is a complete rewrite of all pipelines and analysis, so we effectively started from scratch to produce the data and view that we believe should enhance our ability to find new drug targets.

As part of the re-design, every feature and user journey was scrutinised to understand the cost-benefit of each feature and decide on the minimal viable product that would give us a sustainable impact on target selection.

Unfortunately, the scale and complexity of the change imply that data and services are not backwards compatible. However, most of the use cases should still remain either through similar or different views on the same data.

We are happy to help you and others through this transition. If you have any particular use case, or anything that you would like to do but you don’t know how, please open a new post and hopefully others will benefit from your question.

I hope this helps