Talk:CommunityCurationProtocol

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Revision as of 09:30, 19 May 2008

Multiple similar interactions

How should we display multiple similar interactions in such a way that it looks nice while the interactions are correctly represented? An example is in the Smooth Muscle Contraction pathway:

You see that the interactions to the GNAS protein are grouped by an arc. However, if we just link the lines to the arc, like this:

Then the interactions will not be recognized properly (since there is an interaction with the arc, not with GNAS).

Alternatively, we could explicitely draw each interaction seperately, but as you can see below, this doesn't look nice:

Any ideas on how to solve this?

- Thomas 17:54, 14 May 2008 (UTC)

Can we have each of the separate lines from the receptors link to a connector hub? I'm not sure if this edge connector type exists, but I've seen it illustrated at:

http://www.wikipathways.org/index.php/Pathway:Rattus_norvegicus:Catecholamine_synthesis

This would seem to solve the problem if you can have multiple lines merge into a single line and have anchor points on that line, so that an inhibition edge hits that. I was able to make this in WP, but just to an anchor so it's not a valid hub. I can take or leave the brackets if something like this works.

- Nsalomonis 23:13, 18 May 2008 (PST)

Looks good to me. I went ahead and made the change to the human version of the pathway here so folks can check it out: http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:Smooth_muscle_contraction

-AlexanderPico 07:18, 19 May 2008 (UTC)

Looks great! I'd say this is the perfect solution as visual representation.

The only thing I'm still concerned about is that the line that points to Gnas has a start point that doesn't connect to anything. So what does it mean? (think about trying to convert it to Cytoscape).

I think this demonstrates a flaw in the underlying data model of line anchors. There are now three uses for line anchors, so their meaning is ambiguous:

• A tool to allow representation of mediators of an interaction
• A tool to allow multiple input/output for a reaction
• A tool to group similar interactions (connector hub)

The line anchors are designed to work well for the first use case. But the model isn't optimal for the latter use cases. For example, if you look more closely at the Catecholamine synthesis pathway, you'll see that the way metabolic reactions are stored is a bit odd. There is a single line which start point is connected to one of the substrate and which end point is connected to one of the products. But which substrate to choose if there are multiple? The other substrates are connected to the line that represents the reaction, but do they have a different meaning than the substrate to which the line is directly connected? And how to make a distinction between the enzyme and the reaction input/output? I'm not sure if in the end, we have enough information to derive the real meaning from the current representation. For now, we should just continue to use anchors for all these purposes and use Nathans representation for the problem of similar interactions, because it's certainly improving the pathways. But we should really start defining the actually meaning and find out how to represent it better. One solution we already planned is to allow the user to define interaction type of an edge, but I see now that it doesn't solve everything.

- Thomas 09:30, 19 May 2008 (UTC)