How to access Open Targets with a list of targets and no programmatic skills

You may have read our post on how to Get an association table for your list of genes using the REST API. And thought: "I wish I could search for my list of genes all at once using the web interface".

You are not alone: most of our users access our data from the web interface, and they would like to do the same thing as you.

Due to popular demand, I am happy to announce that Open Targets have released the batch search tool. You can now search for several targets in one go. No programmatic skills necessary plus the added value of intuitive and interactive visualisations.

A use case

I have a list of 26 targets associated with inflammatory bowel disease based on genetics data. How can I search them all in the Open Targets Platform?

Here I will walk you through the new tool for batch search and highlight some of the results that I get.

Go to our homepage and click on the link new batch search, which is below the search box.

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Upload my list (as a .txt or .csv), or copy and paste it into the box. If I paste my list, I will need to give it a name so that I can get back to it later. Hit the Load button:

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Scroll down the page to revise the mappings. There may be genes Open Targets could not map to my list of targets. If that is the case, I may want to double check their names using the suggested matches. I can have my list of targets as HGNC gene symbols or Ensembl Gene IDs. Hit Analyze targets button.

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What results will I get from the batch search tool?

I will get a summary page for my targets divided into four sections:

1) Diseases associated

I can view the diseases classified either by Therapeutic areas (e.g. Immune system disease, Digestive system disease), or divided by the data types (e.g Genetic associations, Somatic mutations) used for the association.

Open Targets rank the diseases according to the probability of finding a disease associated with my set of targets. So I need to look out for the p value.

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2) Pathways

I will find the pathways associated with my targets with a p value available for the ranking.

When I click on the pathway names, e.g. NOD1/2 Signaling Pathway, I will get the pathway diagram and links to Reactome.

3) Drugs

I will get the drugs from ChEMBL that match my list of genes, the target name, the most advanced stage in clinical trials, and the molecule type.

When I click on a drug name, e.g. NATALIZUMAB, I will get general properties of that drug and links to DailyMed and ChEMBL.

4) Interactions between targets

I will get a summary of interactions for my set of targets based on the data from OmniPath DB.

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I can select any two targets in the network and find the details of the interaction between them.

Why not give the batch search a go now?

Try it out with your own list of targets and get in touch by email, Twitter, Facebook or LinkedIn with your comments or suggestions.

I also have this animation on the new tool using the sample list of 56 targets. So you have no excuses for not trying it out, really.

Note that the current limit on the number of targets you can upload (or paste in) is 200. This number is likely to increase with further development of the tool.

Besides the batch search tool, Open Targets have other improvements on web features in the latest release of the Platform, Release 3.0. For more details, check the Release notes.