I wish to parse pathways from NCI/Nature Pathway Interaction Database
into graphNELs. They are available as BioPAX, with an '.owl' file
extension.
Has anybody already done this? I have a start on the task using the
XML package, but don't wish to replicate work already done.
Thanks!
- Paul
I think that Rredland might help, since BioPAX is RDF. I think the
package
even has some BioPAX examples.
Michael
On Wed, May 19, 2010 at 6:26 PM, Paul Shannon
<pshannon@systemsbiology.org>wrote:
> I wish to parse pathways from NCI/Nature Pathway Interaction
Database into
> graphNELs. They are available as BioPAX, with an '.owl' file
extension.
>
> Has anybody already done this? I have a start on the task using the
XML
> package, but don't wish to replicate work already done.
>
> Thanks!
>
> - Paul
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
[[alternative HTML version deleted]]
Hi Michael,
Thanks for the suggestion.
Last I looked, Rredland was a bit of a chore to install on a Mac; it
was enough to deter me. It appears to need librdf and BerkeleyDB.
Has anyone had any luck with installing it on OSX 10.5 or later?
Actually, parsing the owl/BioPAX xml is not -so- hard using the XML
package. But there are quite a few ways the data could be mapped to a
graphNEL. I wonder if anyone has given this any thought....
- Paul
On May 19, 2010, at 6:37 PM, Michael Lawrence wrote:
> I think that Rredland might help, since BioPAX is RDF. I think the
package even has some BioPAX examples.
>
> Michael
>
> On Wed, May 19, 2010 at 6:26 PM, Paul Shannon <pshannon at="" systemsbiology.org=""> wrote:
> I wish to parse pathways from NCI/Nature Pathway Interaction
Database into graphNELs. They are available as BioPAX, with an '.owl'
file extension.
>
> Has anybody already done this? I have a start on the task using the
XML package, but don't wish to replicate work already done.
>
> Thanks!
>
> - Paul
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
On Wed, May 19, 2010 at 9:50 PM, Paul Shannon
<pshannon@systemsbiology.org>wrote:
> Hi Michael,
>
> Thanks for the suggestion.
>
> Last I looked, Rredland was a bit of a chore to install on a Mac; it
was
> enough to deter me. It appears to need librdf and BerkeleyDB.
>
redland now has SQLite back end capabilities, and I have been trying
to find
time to replace the berkeley db interface with interface SQLite. i
will try
to do it in the next few weeks.
>
> Has anyone had any luck with installing it on OSX 10.5 or later?
>
> Actually, parsing the owl/BioPAX xml is not -so- hard using the XML
> package. But there are quite a few ways the data could be mapped to
a
> graphNEL. I wonder if anyone has given this any thought....
>
> - Paul
>
>
>
> On May 19, 2010, at 6:37 PM, Michael Lawrence wrote:
>
> > I think that Rredland might help, since BioPAX is RDF. I think the
> package even has some BioPAX examples.
> >
> > Michael
> >
> > On Wed, May 19, 2010 at 6:26 PM, Paul Shannon <
> pshannon@systemsbiology.org> wrote:
> > I wish to parse pathways from NCI/Nature Pathway Interaction
Database
> into graphNELs. They are available as BioPAX, with an '.owl' file
> extension.
> >
> > Has anybody already done this? I have a start on the task using
the XML
> package, but don't wish to replicate work already done.
> >
> > Thanks!
> >
> > - Paul
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
[[alternative HTML version deleted]]
Hi, Paul
I just added caBIO pathway (including NCI-Nature, Biocarta and
Reactome)
support in GeneAnswers dev version several days ago. The new version
GeneAnswers have two functions, getcaBIOPATHList and
getcaBIOPATHTerms that
can parse caBIO pathways. You might have to manually install the
GeneAnswers
1.5.4 if your Bioc is not 2.7.
Best
Gilbert
On 5/19/10 8:26 PM, "Paul Shannon" <pshannon at="" systemsbiology.org="">
wrote:
> I wish to parse pathways from NCI/Nature Pathway Interaction
Database into
> graphNELs. They are available as BioPAX, with an '.owl' file
extension.
>
> Has anybody already done this? I have a start on the task using the
XML
> package, but don't wish to replicate work already done.
>
> Thanks!
>
> - Paul
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
Hi Paul,
I'm preparing master's thesis related to this subject and my
instructor,
Leo Lahti, pointed me to this discussion. In my study I'm trying to
analyze BioPAX 2 data (from Reactome) to build network of all proteins
that are linked to pathways and also to identify interactions between
proteins based on interactions between pathways and other classes in
Biopax data.
I used Rredland to parse the Biopax owl file on Mac OS X 10.4 and I've
had
no problems with Rredland. Berkeley DB and other dependencies have
been
available through fink project.
When starting the work I had no experience with R but some experience
with
other programming languages. I found the data.frame returned by
rredland
mostly incomprehensible and didn't know much about R packages and the
R
community so I proceeded in writing S4 object model of BioPAX level 2
and
converted the rdf data to graph of objects of my personal BioPAX level
2
implementation. In hindsight, creating this own graph representation
seems
extra work and I think it might have been better to build maybe igraph
or
graphNEL model of the rdf data directly.
Anyway, we have here BioPAX level 2 S4 object model under work and
means
for constructing it from owl file. I have used this object model to
select
only some edges of the BioPAX data to construct simpler graphs
relevant in
my study. If you are interested in the project you can also continue
discussion by email with me (ossi.koivistoinen at iki.fi) or with Leo
(leo.lahti at iki.fi). In particular, we would like to know if there
are
others who could potentially join and contribute to the project but
all
comments and feedback are welcome.
Best Regards,
Ossi
