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BridgeDb Diagram #3

Open AlasdairGray opened 6 years ago

AlasdairGray commented 6 years ago

The current diagram is not immediately interpretable. It has been explained as "BridgeDb is the glue between the top and bottom part" bridgedb

The image does not make clear:

Perhaps it would be clearer to separate the components and connect them with arrows that show the direction of data flows.

DeniseSl22 commented 5 years ago

Hi @AlasdairGray , thank you for the feedback provided. I also don't believe the figure to be easily understood at the moment. Ill take your comments into account, and design a new Figure (perhaps I can make an interactive one with Cytoscape? I'll think of something ;)...). In the meantime, we've been updating the website of BridgeDb. if you have some time, could you take a look, see if your missing anything or have suggestions? Would be much appreciated, thank you in advance :).

Chris-Evelo commented 5 years ago

It is actually more: external data (which should be at the bottom", mapped by BridgeDb using any of the resources/approaches at the current bottom used in resources currently at the top.

Maybe just split it?

BridgeDb is used by these resources to allow mapping of external data. (current top)

BridgeDb uses these approaches and mappings to do so (current bottom)

DeniseSl22 commented 5 years ago

Mhh, I think we can keep it in one network. I came up with the following (just to try it out): image

Size of node is corresponding to In=Out degree; the colours on the edges should indicate which information is going where in the scheme. Ideas on layout are more then welcome :)

DeniseSl22 commented 5 years ago

Chris suggests to make another figure, to show which type of data can be linked through BridgeDb for the tools (bottom layer) mentioned above. I can make such a visualisation as well, but need a bit more time for that (and perhaps I have to split it up for the three "types" of usage I depicted above now with the colours on the edges).

AlasdairGray commented 5 years ago

I suspect that we are trying to give too much detail with the diagram. Who is the audience for this diagram and what information do you need to convey to them? It's probably worth abstracting out some of the complexities and details.

Chris-Evelo commented 5 years ago

The thing with BridgeDb you map one thing with another (e.g. experimental data with pathways or GO, or interacting proteins, or... ). You typically do that in tools and indeed needing the actual mapping data. The second line I just wrote is both diagrams the first is not.