User: Oliver Ruebenacker

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Posts by Oliver Ruebenacker

<prev • 11 results • page 1 of 2 • next >
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BioPAX parsing
... Hello, I created a prototype that can read RDF (using rJava and OpenRDF Sesame) and turn it into a data frame. Then I discovered that Egon Willighagen did almost the same and created RRDF (except that he used Jena instead of Sesame). RRDF does not provide a simple method to get a datafr ...
pathways visualization network graph written 7.5 years ago by Oliver Ruebenacker110
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Comment: C: BioPAX parsing
... Hello Michael, I'm planning to use RJava to drive OpenRDf Sesame, with which I am very familiar. Take care Oliver On Sat, Jun 16, 2012 at 9:54 AM, Michael Lawrence wrote: > Were you guys planning on using Rredland for this? > > > On Sat, Jun 16, 2012 at 3:10 AM, Oliv ...
written 7.6 years ago by Oliver Ruebenacker110
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Comment: C: BioPAX parsing
... Hello, Thanks a lot for the endorsement! I will try to create a prototype in the next days, and then you can probably advice me on how to turn that into a package of desired quality. Take care Oliver On Fri, Jun 15, 2012 at 6:08 PM, Paul Shannon wrote: > Oliver and Martin, ...
written 7.6 years ago by Oliver Ruebenacker110
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Comment: C: BioPAX parsing
... Hello Martin, I don't have code in R to test yet, but I do have extensive experience handling BioPAX in Java, so I'm assuming reading BioPAX using RJava should not be too difficult. The best target format depends on what people would like to do with the data. For visualization, a bi-parti ...
written 7.6 years ago by Oliver Ruebenacker110
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Answer: A: BioPAX parsing
... Hello Martin, I'm currently looking into reading BioPAX into R using RJava and OpenRDF Sesame. If there is interest, I may be looking into submitting a package to BioConductor. It would be very helpful if you could tell me what you need the BioPAX data for, and in what form it would be be ...
written 7.6 years ago by Oliver Ruebenacker110
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Comment: C: Wheat annotation
... Hello, On Wed, Jun 13, 2012 at 10:07 AM, James W. MacDonald wrote: > Unfortunately > anopheles and yeast are the only plants to have jumped that hurdle so far. Neither of these is a plant, though :) Take care Oliver -- Oliver Ruebenacker Bioinformatics Consultant (http:// ...
written 7.6 years ago by Oliver Ruebenacker110
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Comment: C: "graphite" Biocarta 'native' graphs different from Biocarta web site?
... Hello Laurent, On Sun, Jun 10, 2012 at 4:21 PM, laurent jacob wrote: > Hi Oliver, > > 2012/6/10 Oliver Ruebenacker : > >> ?Can you explain some more why you choose not to use Rredland? It >> seems almost certainly relevant for the design of a BioPAX package. >> D ...
written 7.6 years ago by Oliver Ruebenacker110
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Comment: C: "graphite" Biocarta 'native' graphs different from Biocarta web site?
... Hello Laurent, Thanks for the response. To my knowledge, Rredland is not maintained any more. Since I am very familiar with Java (and OpenRDF Sesame), I was thinking of using RJava to drive Sesame. Can you explain some more why you choose not to use Rredland? It seems almost certainly rel ...
written 7.6 years ago by Oliver Ruebenacker110
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Comment: C: "graphite" Biocarta 'native' graphs different from Biocarta web site?
... Hello, On Fri, Jun 8, 2012 at 4:30 PM, laurent jacob wrote: > Hi Hamid, > > 2012/6/7 Hamid Bolouri : > >>>library(NCIgraphData) >>>data("NCI-cyList") >>> NCI.cyList[[1]] >> A graphNEL graph with directed edges >> Number of Nodes = 35 >> ...
written 7.6 years ago by Oliver Ruebenacker110
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BioPAX/SBPAX import for MicroArray Analysis and Hypothesis Building
... Hello Tim, On Thu, May 31, 2012 at 5:53 PM, Tim Triche, Jr. wrote: > this seems clever, although I could swear that an existing package handles > graphical models of similar sorts. We could turn BioPAX/SBPAX into R graphs similar to the way rsbml does it. I wonder if there already ...
microarray network written 7.6 years ago by Oliver Ruebenacker110

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