Question: What Is The Meaning Of Reactome'S 'Set To Member' Reaction Attribute?
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gravatar for sam.neaves
6.9 years ago by
sam.neaves20
United Kingdom
sam.neaves20 wrote:

What is the meaning of Reactomes 'Set to member' Reaction attribute?

In the Reactome diagram key- under reaction attributes, there is a symbol of a dashed line ending with a black circle. What does this mean? I can't see any examples in the human Reactome (I might be being a bit blind here!) and I can not see where this is explained in the manual.

How is this represented in the Biopax level 3 RDF-Owl-XML file?

Thank you for any answers in advance.

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ADD COMMENTlink modified 6.9 years ago by B. Arman Aksoy1.2k • written 6.9 years ago by sam.neaves20
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gravatar for B. Arman Aksoy
6.9 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

I think that diagram style is not being used any more (probably deprecated). When I look at the detailed diagram explanations, I saw this particular screenshot that has the dotted edge style: enter image description here

but when you look at that pathway at its current state, they don't have those styled edges any more:

http://www.reactome.org/PathwayBrowser/#DIAGRAM=109581

So looking at this example, my wild guess is that they represent pathway memberships where you have hiearchical pathways and in them there is an umbrella (top) pathway and it has child pathways to it. In BioPAX these relationships are captured via PathwayComponents; for example take a look at the corresponding "Apoptosis" pathway in Pathway Commons:

http://www.pathwaycommons.org/pc2/get?uri=http://purl.org/pc2/4/Pathway_a9eea90b0e56a117e7f908304ab0f6e0

and simply search for Pathway_a9eea90b0e56a117e7f908304ab0f6e0 to look up the "top" Apoptosis pathway. There, you will see four PathwayComponents that are included in this pathway -- I believe those dotted edges are meant to capture these types of relationships.

Another possibility is the so called "generic" relationships in BioPAX (like AKT representing AKT1/2/3), but I think they are not being visualized in Reactome Pathway Diagram Viewer, but rather being shown on the panel below when you click on a specific entity.

ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by B. Arman Aksoy1.2k

Thank you- I think that makes sense. If that is indeed the case it's a bit confusing why they maintain it in the diagram key if it is depreciated!

ADD REPLYlink written 6.9 years ago by sam.neaves20
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