25.12 Release now live!

[hcornu]

We have just released the latest update to the Open Targets Platform — 25.12

Key stats

Metric	Count
Targets	78,725
Diseases/phenotypes	46,960
Drugs/clinical candidates	18,475
Evidence	32,515,132
Associations	12,010,760

Number of credible sets

Study type	Count
tuqtl	384,849
gwas	1,440,589
sqtl	223,500
pqtl	33,731
eqtl	1,349,418
sceqtl	52,738

Number of unique studies with at least one credible set: 51,805 (GWAS)
Number of unique biosampleIDs (number of tissues/cell-types) from molQTLs: 98

Evidence metrics for this release:

• 3,535,067 genetic evidence from European Variation Archive (EVA)

• 2,976,160 GWAS credible sets from GWAS Catalog, FinnGen through Gentropy

• 5,062 genetic evidence from Gene2Phenotype

• 48,545 genetic evidence from the Genomics England PanelApp

• 3,904 genetic evidence from ClinGen

• 7,189genetic evidence from Orphanet

• 41,264 genetic evidence from Gene burden

• 21,681 genetic evidence from CRISPRBrain

• 6,735 genetic evidence from UniProt Literature

• 9,342 somatic evidence from European Variation Archive (EVA)

• 4,223 somatic evidence from intOGen

• 91,572 somatic evidence from the Cancer Gene Census

• 36,870 somatic evidence from Uniprot

• 569,506 drug evidence from ChEMBL

• 237,329 expression evidence from Expression Atlas

• 10,211 affected pathway evidence from Reactome

• 1,301 somatic evidence from the Cancer Genome Interpreter

• 517 CRISPR-Cas9 (Cancer Cell Lines) evidence from Pacini et al. (2024)

• 1,563,525 mouse model evidence from IMPC

• 23,345,129 scientific literature evidence from co-occurrence mining in Europe PMC

For more details and numbers, read the 25.12 blog post.

[pgodard]

Hi,

Thank you for this new release and making all these data available.

After downloading and checking the data, I think that protein expression (at least per cell type) is missing. It seems to be also the case for mouse model literature references. These information have NA values for a few targets I checked on the web site ( Open Targets Platform , Open Targets Platform )

Is it normal/expected?

[hcornu]

Hi @pgodard and welcome to the Open Targets Community!

Thank you for reporting this. We’ve seen your message and we’re looking into it!

[dsuveges]

Hi @pgodard , Thanks again for reporting this bug! We have addressed the issue at code level and also applied a patch on the released data. Now, all our distributions contains the right dataset: UI, BigQuery, API and FTP.

We have made mayor updates in our data processing pipelines/processes with the last release, so please keep us posted in case you encounter anything suspicious. Thank you.

Best,
Daniel

[pgodard]

Thank you for correcting the issue with protein expression.

However, it seems that references to the literature for mouse models are still missing, as shown below:

Do you plan to correct this? I didn’t notice a corresponding GitHub issue for it.

Thanks again for your support.

[dsuveges]

Hi @pgodard,

The lack of literature references on the Mouse Phenotype widget has been addressed under #4169, however the fix in the data is not rolled out due to a number of complicated consequences. The fix will be out with the next release, which is due around the second half of March.

Sorry for the inconveniences caused.

Best,
Daniel

[pgodard]

Hi @dsuveges ,

Thanks for the follow-up and for having fixed the issue.

Kind regards

Patrice

[jhju]

Dear @dsuveges , @hcornu ,

Thanks for continuing to improve and develop open targets. It has been a great resource for research.

I was checking the tables on BigQuery and noticed that the evidence table only has a little over 1000 rows way fewer than what is shown in the release notes (32,515,132). Could someone verify that the table was uploaded correctly? Thank you!