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monarch-initiative / monarch-legacy

Monarch web application and API
BSD 3-Clause "New" or "Revised" License
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Add phenotype comparison for homologs #1162

Open mellybelly opened 8 years ago

mellybelly commented 8 years ago

I want to somehow see the phenotypes of the the homologs and how they compare to the gene page that I am on. Not sure if this is a new instance of phenogrid or how to display this, but its clear we need some mechanism to have an overview of the phenotypic similarity between orthologs across species.

nlwashington commented 8 years ago

some related tickets includes #325, https://github.com/monarch-initiative/phenogrid/issues/135, #20, #363, #567.

nlwashington commented 8 years ago

also, can we reuse the code that produces the ortholog comparison on the analyze page for this, @kshefchek ?

nlwashington commented 8 years ago

Also, I think this is hugely important as well. Can this be placed on the homologs tab?

nlwashington commented 8 years ago

Implementing this properly will enable us to have a flexible grid to display any collection of genes (say, from pathways or drug targets or grouped by any mechanism)

harryhoch commented 8 years ago

Let's discuss on Thursday's call.

kshefchek commented 8 years ago

I think we have a few options here, we could have a button that minimizes the table to a two or three column subject object table and generates a phenogrid on the right hand side. We could also do something similar but instead of a phenogrid have a "minipage" with various tabs where the context is controlled by two column table.

jmcmurry commented 8 years ago

For now, even something that collapses everything into a single table, visualization aside, would be better than nothing. Let's consider that the scope of the ticket to be addressed; unless there are suggestions.

kshefchek commented 8 years ago

If left as a table view what column(s) would we add? Phenotypic similarity and maybe phenotype count?

jmcmurry commented 8 years ago

@mellybelly With the "homolog phenotypes" tab we are now closer to being able to address this. Please discuss requirements for where to go from here.

kshefchek commented 8 years ago

Both phenogrid and monarch app support this, it is similar to analyzing a set of phenotypes against orthologs on the analyze page. However, with 5 species in phenogrid, another column may add some clutter, so we should think carefully about how to display this.

Another option would be to run an analysis every time we load our data and cache cases where phenotypes are conserved across species (via some owlsim cutoff). We could then display this on the overview page. This is more in line with our vision for an enhanced overview page that tells a story about the data.

jmcmurry commented 8 years ago

Related to https://github.com/monarch-initiative/monarch-app/issues/363 and https://github.com/monarch-initiative/monarch-app/issues/1353