Hi there,
I am submitting a bug report for the Open Targets Platform. I searched for a variant and was looking at the GWAS credible set list to find the L2G predictions, but it was not showing up on the webpage and I am not able to access any data via a GraphQL API query script. Thank you for your help.
Can you help us reproduce your problem? Can you give us a GraphQL API query or variant that it’s not showing in the webpage?
Also, remember the Open Targets Platform only contains variation associated with a phenotype. Not every possible variant would be represented in the Platform.
In the Open Targets Platform, a variant refers to any human variation associated with a disease, trait or phenotype that has been reported in any of our sources.
More info in documentation
Hi there,
Here is the script I am using and the variant I was attempting to look up:
variantId ← “2_59928185_A_T”
Hi @mjatoi,
Indeed there was an issue with the web application that was not handling a case when some of the credible sets might not have any L2G prediction > 0.05. We are resolving the problem in the web application.
However, this should not prevent you from querying the information from the API. I checked the response and there are 8 different GWAS credible sets that contain your variant of interest. What might be a problem in this case is that none of the credible sets have L2G predictions above 0.05, therefore the model is not even weakly confident about the gene assignment, most likely due to the lack of protein coding genes in the region.
We are thinking about expanding the L2G model to non-coding genes, but we want to be confident about the assignments before rolling them out to the Platform.
I hope this helps