search

monarch-initiative / monarch-legacy

Monarch web application and API
BSD 3-Clause "New" or "Revised" License
42 stars 37 forks source link

dendogram similar profile viewer #182

Open nlwashington opened 10 years ago

nlwashington commented 10 years ago

users should be able to view a set of annotated entities (genes, genotypes, diseases, whatever) in a dendogram viewer.

http://bl.ocks.org/mbostock/4063570

this could be separate or in addition to the matrix view.

on a disease page, this could be displayed as the "closest" diseases (or models or whatever), as a "phenotypic neighborhood". the user should be able to zoom in/out on the disease neighborhood. obviously, this is effectively what a tree view overlaid on the ontology would give you. but it's possible that when build de novo from phenotypes, it would be different. this ought to be possible given any set of annotated entities (including a set of annotations delivered to the server on-the-fly).

the data would need to be computed and served from our the owlsim server.

on the owlsim side, we ought to precompute these for the diseases, genes, and genotypes that already exist. the default would be to output the result in newick format (the standard), but could be served in json format.

perhaps something like

https://github.com/sape/hac/tree/master/src/ch/usi/inf/sape/hac/dendrogram

or (in a discussion with chris) even a cytoscape viewer of closely-related diseases/models/genes/pathways. let's discuss soon.

nlwashington commented 9 years ago

maybe we can dust off the old code that was written to do this?

jmcmurry commented 9 years ago

Now in process of reviving discussions of the neighborhood view site-wide. It would be good to know what's in place on the owlsim and scigraph backends. @nlwashington @kshefchek ?

harryhoch commented 9 years ago

definitely worth considering in the context of the ontology navigation discussion