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Complex-Portal / complex-portal-view

This project is a new implementation of the former Complex-View. For the development we used Angular-CLI and TypeScript.
www.ebi.ac.uk/complexportal
Apache License 2.0
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Molecule Set symbol in viewer and legend don't match? #201

Open colin-combe opened 3 years ago

colin-combe commented 3 years ago

I'm submitting a ... (check one with "x")

[x ] bug report => search existing issues for a similar problems/requests
[ ] feature request
[ ] support request => Please do not submit support request here, instead see: http://www.ebi.ac.uk/support/intact

Current behaviour Molecule sets have double-outline, rounded-corner rectangle as symbol in viewer but octagon as symbol in legend

Expected behaviour same symbol in both, could be that octagon is right one and viewer is wrong

Minimal reproduction of the problem with instructions visit https://www.ebi.ac.uk/complexportal/complex/CPX-5183

What is the motivation / use case for changing the behaviour? the symbols don't match btw figure and legend

Please tell us about your environment: chrome, linux

bmeldal commented 3 years ago

Colin, you are right, I never noticed this! The symbol in the viewer is the correct one (same as Reactome), legend needs fixing.

@noedelta @EliotRagueneau

We should also check this in the new IntAct beta as it also uses sets.

EliotRagueneau commented 3 years ago

We already noticed this issue. Basically, we wanted to align IntAct style between the desktop Cytoscape application and the website, but the thing is that the Cytoscape desktop doesn't support yet double-layered pill shapes, so we used octagons instead. We are currently looking with Cytoscape developers if it is possible to add this new shape so that we can homogenise our symbols with Reactome ones. If they do accept, we will change the legend in the interaction and the network viewer. If they refuse, it might be great to update the complex-viewer to use octagons instead.

First, let's see Cytoscape answer to that :D

colin-combe commented 3 years ago

If they refuse, it might be great to update the complex-viewer to use octagons instead.

that would be fine - though I think the octagons are easily confused with the hexagons sometimes used for a sub complex

EliotRagueneau commented 3 years ago

Noe had the same concerns, though I think it's not too bad because, in a way, complexes and molecules sets are both a kind of collection of molecules, just one being AND and the other OR. But yeah it's better if they are clearly distinguishable

bmeldal commented 3 years ago

Reactome had to make up the symbols, too, as SBGN doesn't have one for sets either.

This issue resurfaces time and again < sob >

bmeldal commented 3 years ago

I had the same conversation with the Covid disease map folks. I think it's time everyone acknowledges that we need these symbols as standards across all biological visualisation platforms/software...

This is broken AND needs fixing - by the whole community.