What happened to the batch search functionality?

With the release of the next-generation Platform on 29 April 2021, we made the decision to deprecate the batch search functionality while we work on a replacement approach.

We made this decision because the existing batch search API endpoint and user interface was not optimised to support complex queries and on-the-fly association scoring.

While we work on a new approach, users can perform batch search queries using our comprehensive list of datasets available for download. For more information on how to use the Platform data downloads, including sample Python and R scripts, please visit our data downloads documentation page.

The Platform team have started to work on a replacement batch search functionality and we want to know what data Platform users would like to see in a batch search view.

Previously, our batch search view included:

  • List of associated diseases
  • List of enriched pathways
  • List of enriched Gene Ontology terms
  • Tractability analysis for targets
  • List of drugs
  • Interactions between genes

What data and/or analysis would be useful in a batch search view to support target identification and prioritisation?

Hi Hercules. Again thank for your great job(s).
Let me say, in order, we used:
1.Gene interaction
2.pathways
3.Associated diseases
4.drugs

Now we’are also approaching mrna sirna ecc, to increase complexity of course starting from gene-symbol (sirna for part similarity). Let you know

many of us, who do not know how to program, hope that batch search functionality will soon return. This type of search was not only fundamental but one of the most useful things that could be found on the web. Its ease of use combined with the enormous amount of information, especially that related to clinical and disease, made it unfortunately irreplaceable. Today for us this value is lost. I hope you can focus on this outcome as soon as possible.

Hi @angrist, we are working on different options for batch search as we know it is very popular.

Could you please rank which sections of the batch search were most useful to your work and explain why?

  • Gene symbol mapping
  • Associated diseases
  • Pathways
  • Gene Ontology
  • Tractability
  • Drugs
  • Interactions between targets

Are there other types of analyses that would support your target identification and prioritisation research questions?

Thank you :grinning:

Dear Hercules,

Gene Mapping
Pathway
Drugs and diseases

Do you have any dates regarding when the system will be available?

Thank you,
D

@DavideG, thank you for your insights into how you use batch search. We do not have a confirmed timeline for the return of batch search, but will post more details when they become available.

In the meantime, my colleague @irene has written a post with a BigQuery script that you can use and adapt to replicate batch search. Please see Get marketed drugs for a set of targets with BigQuery.

Hello Andrew,

The original intent of the batch search was to aggregate information and extract patterns for repeated routine questions that non-data scientists have in early drug discovery.

Usually, investigators will come with a list of genes and won’t have time to look at the platform gene by gene. List size can scale up to several hundred genes:

  • Is there any gene associated to tool compounds?
  • Is there any launched drug associated to my list of genes? Is there any clinical trials?
  • Is there any safety concern by targeting these genes?
  • Where are my gene expressed? (baseline expression in tissues and cell types)
  • Do I see any significant enrichment in:
    a) specific disease areas
    b) pathways/GO terms
    c) specific type of evidence from the platform
  • From my list of genes, which ones have been highly cited, normally cited, lowly / not at all cited in the literature.

So, similar questions to the gene profile page of the platform but aggregated and analysed for a better overview.
More advanced questions could be answered.

Best regards,