July update: Summer Platform Release, Standalone Deployment, AI and Immunology

Here in the UK, I’m fairly sure summer has now been and gone — I hope it’s sunny wherever you are reading this from! In this edition, catch up on our Platform Summer release, let us know what single-cell data you’re most interested in, read about how AI is changing immunology research, and discover our Platform standalone deployment tool.

Not putting the sunscreen away just yet,

Helena

24.06 Platform release introduces an upload function for entity lists

The Open Targets Platform Summer Release (24.06) is out now! You can now upload lists of entities to customise the associations view.

A much requested feature, this allows you to easily compare the evidence for the specific target-disease relationships you are interested in. Data-wise, this release integrates the latest data from AstraZeneca’s PheWAS Portal (v5), as well as new ancestry-specific gene burden evidence for prostate cancer, and expanded schizophrenia data from the SCHEMA consortium. We’ve updated to ChEMBL 34, which now integrates data from the European Medicines Agency, and added the Gene2Phenotype skeletal panel contributing 328 new target-disease associations.

Read the release blogpost.

What is the top question we should address from single-cell data?

Our latest Integration Day (pictured above: Annalisa Buniello's talk) was a chance to reflect on some of the recent work we've done using single-cell sequencing, and think about potential future work in this space.

We have just launched a poll on social media — what is the most important question we should address from single-cell data?

Let us know what you think on Twitter or LinkedIn.

AI and Immunology

Open Targets Scientific Director Gosia Trynka shared her thoughts on AI and Immunology in Immunity’s Voices (note this is not open access).

Posting on LinkedIn about the article, Gosia said:

The immune system is beautifully complex and dynamic to fulfil its role and defend us from external pathogens.

I see a great opportunity for AI to bring together the existing knowledge, integrate it with rich large-scale experimental datasets and apply complex modelling to help us interpret the data, build hypotheses, and predict outcomes.

Introducing the Standalone Deployment Tool

Want to tinker with the Open Targets Platform to add your own data or tools? Need to check past versions of the Platform?

Alongside our 24.06 release, we have released a new standalone deployment tool, which allows you to deploy any Open Targets Platform release since March 2023 locally, anywhere, with just three commands.

Read the full post on the Open Targets blog or watch Manuel Bernal Llinares introduce the tool on YouTube.

Interested in joining Open Targets? We are currently recruiting:

• Technical Specialist, Wellcome Sanger Institute (16 June) — A new Open Targets project aims to examine the intricate interplay between immune cells, cancer-associated fibroblasts (CAFs), and malignant cells by applying single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics (STx), and WGS on samples from colorectal patients before and after treatment.
• Biocurator, EMBL-EBI (21 July) — The new open-source Perturbation Catalogue project for harmonised and curated human gene, variant, and expression data is an opportunity to rise to the challenges of ‘big data’ and make contributions that advance the reach and utility of sequence data.

Keep an eye on our jobs page for all our opportunities.

I’d love to know what you think of this newsletter — let me know at [email protected]!

— Helena, Open Targets Communications Lead