Document how to programmatically visualize a bbop-graph

[cmungall]

This is stale: http://wiki.geneontology.org/index.php/AmiGO_2_Manual:_Visualize_Freeform

This doesn't work visualize

Motivation: https://github.com/monarch-initiative/monarch-app/issues/1232#issuecomment-209572296

[kltm]

Put this in the AmiGO tracker--AmiGO's visualize is completely unrelated to bbop-graph.

[kltm]

Ah, more context from the other ticket.

This ticket is now to document visualizing bbop-graph. Could you add the JSON you're trying to this ticket? As well, take a look at the docs, I think you want to be looking at "graph_data".

[cmungall]

The JSON is in the Monarch ticket

But this ticket is about a more general issue. We have an awesome graph format, with an even more awesome ecosystem of libraries and services around it. The README should have a small collection of links to help orient people: what is a bbop-graph, what things spit them out, what things consume them? The README assumes you're a developer wanting to introspect a bbop graph directly but there are a wider range of consumers.

will happily help with this, just not sure of yr grand plan. No rush, just noting for the future.

[kltm]

Okay, I see what is going on now.

The main AmiGO graph viewer is tuned to what's loaded in GOlr, allowing people to use shorthands at various levels of detail. It is not a general graph viewer. The formats are similar, but the one you're trying to use uses an historical format, not the general bbop-graph JSON form.

That said, it is backed by a general graph maker. Said viewer has a client in labs, but has not been generally "released":
http://tomodachi.berkeleybop.org/visualize?mode=client_freeform
If you want, I could pretty easily "graduate" this and add it to 2.5. I think the only outstanding issue is geneontology/amigo#216.

[kltm]

Pinging @cmungall , as current formulation of ticket is invalid. (Not stale as it is a different format entirely.)