Tool: Open Targets batch search, your list of human genes matched to our disease associations
7
gravatar for Denise - Open Targets
2.4 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

You may have used our intuitive, interactive, and free-to-use Open Targets Platform to search for disease associations for a gene, on a one-by-one case basis.

Now we are pleased to announce the Batch search tool. Upload your target list and no more search on a one-by-one basis: search for hundreds of genes in one go and get our Open Targets data summarised as follows:

  • Disease associations

View the diseases associated with your genes (our proxies for drug targets).

You can view the disease associations by Therapeutic areas (e.g. Immune system disease, Digestive system disease), or by data types supporting the association (e.g. Somatic mutations, RNA expression, etc).

We rank the associations based on the probability of finding a disease associated with your set of targets. Look out for the p value in the table results.

  • Pathways

Get the pathways that are associated with your genes and rank them according to the p value we provide.

If you click on a pathway name, you will get to eye-catching images as Summary page for pathway Immune System, for example. We also link this information to our original data source, Reactome.

  • Gene Ontology Get the GO terms enriched in your list of targets, ranked by the relevance p value.

  • Drugs

Find the drugs from ChEMBL that match your list of genes. We also provide the target name, the most advanced stage of clinical trials the drug is in, and the molecule type (e.g. antibody).

If you click on a drug name, you will get the general properties of that drug and external links to DailyMed and ChEMBL in our Summary page for drug NATALIZUMAB.

  • Interactions between targets

View the summary of interactions for your set of targets. These interactions are based on OmniPath DB, a literature curated human signalling pathways.

Select any two targets in the network and find the details of the interaction between them.

What else you need to know

Accepted formats:

.txt .csv or simple copy and paste from a spreadsheet.

Who is this tool for:

It is for everyone with or without programmatic skills.

Bonus:

Funky visualisations and direct links to other facets in the Platform. See it for yourself with our Open Targets: search for many targets at once with our batch search tool GIF animation.

Upper limit:

We accept up to 200 genes but are currently working on increasing this upper limit.

In the meantime, if you have more than 200 genes, you can use our REST API for programmatic access of Open Targets data. Have a look at our blog post for a tutorial on how to Get an association table for your list of genes programmatically.

Comments or suggestions?

We want to know how you get on with our batch search tool. So reply to this post or get in touch by email.

Alternatively check our help page on the Batch search tool or head to our YouTube channel to watch a quick tutorial on how to search for several targets at once with Open Targets, using the "Greatest hits of the human genome" as a example of a list of genes.

ADD COMMENTlink modified 13 months ago • written 2.4 years ago by Denise - Open Targets5.0k
2

Nice! Turning out to be a good open source competition for IPA.

ADD REPLYlink written 2.4 years ago by genomax72k
2

I liked using Open targets and how it was being developed. This is a great improvement. About the competition with IPA I still cannot say much as the knowledge base of IPA for pathway curation is their own recipe . They have really pulled a lot of experimental information but will never clarify them well. To be honest IPA for me still runs as a front runner for pathways specifically when you can used the information of directionality. Reactome on the other hand is really amazing and so is Open target evolving. But I like the fact of drug gene association. An sure open targets will be much more resourceful in future and specially not everyone will use IPA or afford it. I use IPA a lot but I will always prefer open source tools. Personally not yet made a comparison of the tools but it will be worth to do it . Congratulations to the Open targets team to incorporate new features. I have always liked the project and the vision associated with it.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by ivivek_ngs4.8k
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