Question: RSBML wrong edges
0
gravatar for tjal0001
6 weeks ago by
tjal00010
tjal00010 wrote:

Hi, I am using rsbml package in R to create a biological network in R. The problem is that it seems rsbml extracted wrong edges:

I created a graph using the following code:

g <- rsbml_graph(doc)

But I see edges are wrong. In cell designer, I have an edge from species 's2428' to 's2421'. But in the outcome of the following code, I have just 're629' and 're623'.

for (i in seq(1, length(distinctEdgeNum),by = 1)){
  z=distinctEdgeNum[[i]]
  if (from(z)=='s2428'){
print(z)}
  else if  (to(z)=='s2428'){
   print(z)}}

First of all, I searched the Cell designer model and there is no 're629' and 're623' in the model. Second, why the correct edges are not extracted! I HIGHLYYY appreciate if someone could help me with this critical issue. distinctEdgeNum is generated using following code:

 distinctEdgeNum=buildEdgeList(g)

Kind Regards,

rsbml R celldesigner • 97 views
ADD COMMENTlink modified 26 days ago by Michael Lawrence11k • written 6 weeks ago by tjal00010

Please provide a reproducible example, i.e., an example SBML file that demonstrates the problem.

ADD REPLYlink written 6 weeks ago by Michael Lawrence11k

Hi Michael,

Thanks for always helping me. I am working with mTOR signalling pathway and following are the codes: I added first two lines in case you need to install rsbml.

If you check the graph, you can see multiple edges specially between species started with 's' are not included in the graph!

Kind Regards,

ADD REPLYlink modified 4 weeks ago • written 6 weeks ago by tjal00010

Where can I get that file?

ADD REPLYlink written 6 weeks ago by Michael Lawrence11k

Sorry for delay Michael. Please find the file in the following link:

https://drive.google.com/open?id=11MM169V7H1wbt-51YfUbG0I5EnPh1f7G

ADD REPLYlink modified 4 weeks ago • written 5 weeks ago by tjal00010

I appreciate if someone could help me to understand the logic. I've read the documentation as well but have no idea why edges that I'm after are not retrieved?!

Kind Regards,

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by tjal00010
Answer: RSBML wrong edges
0
gravatar for Michael Lawrence
26 days ago by
United States
Michael Lawrence11k wrote:

Cell Designer uses a different graph representation of the SBML model. The rsbml package generates a bipartite graph connecting species to reactions. The "re" identifiers refer to reactions. It sounds like Cell Designer is directly connecting reaction participants. You could collapse the rsbml graph into the Cell Designer graph by just removing the reaction intermediates.

ADD COMMENTlink written 26 days ago by Michael Lawrence11k
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