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monarch-initiative / monarch-legacy

Monarch web application and API
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interaction connectivity graph #370

Open nlwashington opened 10 years ago

nlwashington commented 10 years ago

i think it'd be great to see a connectivity graph on the interactions tab. perhaps use a force-layout? right now the interactions are only drawn from biogrid, but we could get them from string in the near future. i think this can be done with the data we have now, before we have the fancy grid explorer that would come from sci graph.

cmungall commented 10 years ago

Only showing gene-interactions? Don't think it should be too hard but it wouldn't add so much value over what's on other sites unless we overlay things somehow

kshefchek commented 10 years ago

Is this in reference to the interactions tab on the gene page? I think for this to work we would need to pull out additional interaction and/or pathway data. Otherwise, since we're just listing all binary interactions for a single gene, the graph would look like a large circle with the query gene at the center. I create a simplified example with data from tartini.crbs.ucsd.edu/gene/NCBIGene:975 : http://bio-grapher.appspot.com/prototype

harryhoch commented 10 years ago

Agree with @cmungall here. This is not hard to do, but in the end is very low in the data/screen-space ratio.

On 23 May 2014, at 1:25 PM, kshefchek notifications@github.com wrote:

Is this in reference to the interactions tab on the gene page? I think for this to work we would need to pull out additional interaction and/or pathway data. Otherwise, since we're just listing all binary interactions for a single gene, the graph would look like a large circle with the query gene at the center. I create a simplified example with data from tartini.crbs.ucsd.edu/gene/NCBIGene:975 : http://bio-grapher.appspot.com/prototype

— Reply to this email directly or view it on GitHub.

Harry Hochheiser University of Pittsburgh Department of Biomedical Informatics harryh@pitt.edu 412 648 9300

jmcmurry commented 9 years ago

A couple of questions:

  1. We don't have an interactions tab anymore; was this refactored to 'pathways'?
  2. It sounds like there wasn't consensus that this was a high priority; could we close it? --- If not, are the specifications different than they were originally? Eg. overlay?
harryhoch commented 9 years ago

@jmcmurr - I think we need to take a step back and discuss goals and use cases.

nlwashington commented 9 years ago

interactions data was missing from golr. this has been now added to scigraph/golr in commit https://github.com/monarch-initiative/configs/commit/e5af70c336bc4104abb5e22f0e05d373e3a70691.

please note that i have now also added paths for colocalization, regulation/causality, physical adjacency.

jmcmurry commented 8 years ago

overlaying gene interaction networks with a collection of phenotypes is pretty easy to do with the sankey D3. Let's at least revisit and scope this as part of data visualization efforts.