return human genes most similar to a set of input phenotypes

[nlharris]

Conversation in Slack:

Matthew Brush
I am on a Translator mini-hackathon call now, and we are discussing a use case where we start with a set of patient phenotypes and look for possible treatments. I'm exploring how Monarch's phenotype similarity tool may be useful here. One thing I couldn't figure out how to do is to go from a set of HP terms, to a set of human genes with the most similar phenotype profiles. Is this doable . . . the tool in the UI allows you to select various model organism taxon for a gene similarity search - but not humans. See screenshot below. (edited)

Tim Putman
That does seem to be the case that you can't select human for the result set.
Here is the api call you could make to do what you are asking:
https://api-gcp.monarchinitiative.org/api/sim/search?&id=HP%3A0001639&id=HP%3A0100542&id=HP%3A0001572&id=HP%3A0001537&id=HP%3A0001510&id=HP%3A0001508&id=HP%3A0001511&taxon=9606

Matthew Brush
Hi Tim . . . all the matches in the api results above are of type "disease" . . . I am looking for matches of type human gene.
is there an api call that would get me that info?

@putmantime
There doesn't appear to be a way to return human genes as the results, the difference in the API call between "All Matching Genes" and "All Matching Diseases" is just the taxon being set to 9606 for the latter.
If it's a model org taxon id the results are genes, if it's human it's diseases

Tim Putman
We are looking into being able to set a result category in the API
Meantime there are other ways with code to do this that we could chat about

Matthew Brush
Thanks Tim. I would think that being able to return human genes most similar to a set of input phenotypes would be generally useful - and hope that this functionality could be added to the Monarch UI and the API at some point.