I am trying to query a gene and look only for associations with diseases and phenotypes of interest to me. In other words, does my gene have a genetic association with anything in this specific SET of diseases and phenotypes?
Building associations based on all available evidence for a set of diseases is not something that can be done through the Platform at the moment. However, this is an important functionality and we have worked on a prototype with satisfactory results.
We have recently discussed the case of FINERENONE a NR3C2 inhibitor approved by the FDA in 2021 for the treatment of chronic kidney disease. The association page has no indication of a genetic link between CKD and NR3C2. However, there is a genetic link between NR3C2 and albuminuria and early sign of kidney failure. The use-case proposed here would be to produce a combined prioritisation by using both CKD and albuminuria (as well as potentially other kidney-related traits).
A different story is how you find what are the most relevant phenotypes associated with your disease of interest. This is a problem that it’s not resolved at the moment, although different people inside and outside Open Targets. In the next few months, we will most likely work on this topic as it’s a necessary step to unblock the above.
I know that Open Targets diseases and phenotypes are based on the EFO, but is there a complete list somewhere of diseases and phenotypes that could show up in the Disease/Phenotype table?
I presume your question is what is the full list of searchable diseases or phenotypes. The EBI SPOT team that develops and maintains EFO has a service named OLS in which you can browse the EFO ontology as well as many other ontologies.