FWIW I have added Biopax level3 owl/rdf to current image of Rredland -- I
think you can get it via bioc devel svn with the usual credentials
readonly/readonly.

If we run the Rredland.Rnw

> bp3m
RDFModel instance
> as(bp3m, "data.frame") -> bp3df
> dim(bp3df)
[1] 1611    3
> as(bp3m, "graphNEL") -> bp3g
> bp3g
A graphNEL graph with directed edges
Number of Nodes = 554
Number of Edges = 1606
> nodes(bp3g)[1:10]
 [1] "<http://www.biopax.org/release/biopax-level3.owl>"
 [2] "<http://www.biopax.org/release/biopax-level3.owl#absoluteRegion>"
 [3] "_:r1339811872r5333r238"
 [4] "_:r1339811872r5333r239"
 [5] "<http://www.biopax.org/release/biopax-level3.owl#DnaRegionReference>"
 [6] "_:r1339811872r5333r240"
 [7] "<http://www.biopax.org/release/biopax-level3.owl#RnaRegionReference>"
 [8] "<http://www.biopax.org/release/biopax-level3.owl#author>"
 [9] "<http://www.biopax.org/release/biopax-level3.owl#availability>"
[10] "<http://www.biopax.org/release/biopax-level3.owl#BindingFeature>"
> adj(bp3g, "<
http://www.biopax.org/release/biopax-level3.owl#RnaRegionReference>")
$`<http://www.biopax.org/release/biopax-level3.owl#RnaRegionReference>`
[1] "<http://www.w3.org/2002/07/owl#Class>"

[2] "<http://www.biopax.org/release/biopax-level3.owl#EntityReference>"

[3]
"_:r1339811872r5333r366"

[4] "<http://www.biopax.org/release/biopax-level3.owl#DnaReference>"

[5] "<http://www.biopax.org/release/biopax-level3.owl#DnaRegionReference>"

[6] "<http://www.biopax.org/release/biopax-level3.owl#ProteinReference>"

[7] "<http://www.biopax.org/release/biopax-level3.owl#RnaReference>"

[8] "<http://www.biopax.org/release/biopax-level3.owl#SmallMoleculeReference>"

[9] "\"Definition: A RNARegion reference is a grouping of several RNARegion
entities that are common in sequence and genomic position.  Members can
differ in celular location, sequence features, mutations and bound
partners.\"^^<http://www.w3.org/2001/XMLSchema#string>"

So various useful transformations are available with the Rredland package,
that I withdrew from distribution
because I wanted to expose more of the librdf RDF model query facilities
and that takes more work than I have had
time for.

On Fri, Jun 15, 2012 at 6:08 PM, Paul Shannon <pshannon@fhcrc.org> wrote:

> Oliver and Martin,
>
> It would be very helpful to have easy access to BioPAX data in
> Biocondcutor.
>
> Just now, at the weekly Bioconductor dev-team meeting, we discussed your
> ideas, and want to endorse them.  Oliver's proposal to parse the RDF
> triples into a data.frame has lots to recommend it.  It would be
> immediately useful, and yet also allow for more sophisticated uses later.
>  With these relationships in R, annotated as BioPAX data often are, we can
> imagine interested parties writing S4 classes which use the data, which
> might provide flexible querying capabilities, and be able to transform
> those triples into graphs and networks, for further computation and display.
>
> Please let us know if we can help.
>
> - Paul
>
>
> On Jun 15, 2012, at 12:23 PM, Oliver Ruebenacker wrote:
>
> >     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-partite graph in a popular
> > graph-layout package should be best. Is there any particular graph
> > package in BioConductor or R in general you would recommend?
> >
> >  For actual analysis, people probably have more specific requirements.
> >
> >  BioPAX is a format based on RDF/OWL, which in turn is based on
> > organizing data in triples, which could be stored in a three-column
> > data frame (or perhaps a fourth column for data type). For example
> > (incomplete, for illustration only):
> >
> >  ex:mapPhosphorylization   rdf:type   bp:BiochemicalReaction.
> >  ex:atp   rdf:type   bp:SmallMolecule.
> >  ex:adp   rdf:type   bp:SmallMolecule.
> >  ex:map   rdf:type   bp:Protein.
> >  ex:mapPhosphorylized   rdf:type   bp:Protein.
> >  ex:mapPhosphorylization   bp:left   ex:atp.
> >  ex:mapPhosphorylization   bp:left   ex:map.
> >  ex:mapPhosphorylization   bp:right   ex:adp.
> >  ex:mapPhosphorylization   bp:right   ex:mapPhosphorylized.
> >
> >     Take care
> >     Oliver
> >
> > On Fri, Jun 15, 2012 at 3:03 PM, Martin Preusse
> > <martin.preusse@googlemail.com> wrote:
> >> Hi Oliver,
> >>
> >> I think there is a lot interest in a bioconductor package!
> >>
> >> Personally, I would like to read pathways stored in the BioPAX format
> into any kind of graph. It's a philosophical question if reactions should
> have nodes or should sit on the edges :) So far I have not used any R graph
> package. But I assume there are some very generic packages which are
> flexible enough to support both direct and bi-partite pathway structure. I
> used e.g. the JUNG graph API for JAVA extensively.
> >>
> >> I'm not sure what you mean with RDF/OWL triples. For me BioPAX is only
> a format to store a pathway. And I would like to bring it back into its
> natural form: a network!
> >>
> >> Do you have any code to test? I have used RJava before. All this RDF
> and XML file format stuff kind of puzzles me though … :)
> >>
> >> Cheers
> >> Martin
> >>
> >>
> >>
> >> Am Freitag, 15. Juni 2012 um 18:32 schrieb Oliver Ruebenacker:
> >>
> >>> 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 best for you. Possible
> >>> options are:
> >>>
> >>> - A data frame of the RDF/OWL triples
> >>> - A graph of the RDF/OWL triples
> >>> - A data frame with one row for each reaction-participant
> >>> - A bi-partite graph with nodes for reactions and nodes for substances
> >>> - A with nodes for substances only, with edges for interactions
> >>> - A genetic interaction graph
> >>>
> >>> This list is roughly sorted form the one most easy to the most
> >>> difficult to provide.
> >>>
> >>> Take care
> >>> Oliver
> >>>
> >>> On Thu, Jun 14, 2012 at 10:01 AM, Martin Preusse
> >>> <martin.preusse@googlemail.com (mailto:martin.preusse@googlemail.com)>
> wrote:
> >>>> Many biological pathway resourced provide their data in the BioPAX
> format (http://www.biopax.org/index.php), a special XML format for
> biological interaction networks. Examples are pathway commons (
> http://www.pathwaycommons.org/pc/) and Reactome (http://www.reactome.org (
> http://www.reactome.org/)).
> >>>>
> >>>> A JAVA library for parsing BioPAX files exists:
> http://www.biopax.org/paxtools.php
> >>>>
> >>>> Has anybody used BioPAX files with R? Is it possible to read BioPAX
> files in any R based graph structure? A solution similar to the KEGGgraph
> package for KEGG pahways would be great, since more and more databases
> start using BioPAX.
> >>>>
> >>>>
> >>>> Any ideas are appreciated!
> >>>>
> >>>> Cheers
> >>>> Martin
> >>>>
> >>>> _______________________________________________
> >>>> Bioconductor mailing list
> >>>> Bioconductor@r-project.org (mailto:Bioconductor@r-project.org)
> >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> Oliver Ruebenacker
> >>> Bioinformatics Consultant (
> http://www.knowomics.com/wiki/Oliver_Ruebenacker)
> >>> Knowomics, The Bioinformatics Network (http://www.knowomics.com)
> >>> SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
> >>>
> >>
> >>
> >>
> >
> >
> >
> > --
> > Oliver Ruebenacker
> > Bioinformatics Consultant (
> http://www.knowomics.com/wiki/Oliver_Ruebenacker)
> > Knowomics, The Bioinformatics Network (http://www.knowomics.com)
> > SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
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> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

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