Open nlwashington opened 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
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
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
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Harry Hochheiser University of Pittsburgh Department of Biomedical Informatics harryh@pitt.edu 412 648 9300
A couple of questions:
@jmcmurr - I think we need to take a step back and discuss goals and use cases.
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.
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.
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.