Hi Weijun,

Interesting tool pathview, is there any plans to extend its capabilities
I/O to handle SBML files?

People from metabolic modelling would probably benefit a lot from that
extension, and SBML is more or less the reference input file in
pathway/metabolic analysis.

Regards,

Pj


2013/9/3 Oleg Moskvin <moskvin@wisc.edu>

> Hi Weijun,
>
> This works perfectly as expected! Thank you for the fast update. This
> option is indeed destined to be very useful for many researchers.
>
> Best,
>
> Oleg
>
> On 08/30/13, Luo Weijun  wrote:
> > The updated pathview (version 1.1.5) is now available through BioC devel
> version:
> > http://bioconductor.org/packages/2.13/bioc/html/pathview.html
> > R-forge version failed to build because they haven’t installed some
> dependency package with their new R 3.0.1. I’ve contact their admin, but
> not sure when this can be solved.
> > Weijun
> >
> > --------------------------------------------
> > On Wed, 8/28/13, Luo Weijun <luo_weijun@yahoo.com> wrote:
> >
> > Subject: Re: [BioC] pathview puzzle
> > To: "Oleg Moskvin" <moskvin@wisc.edu>
> > Cc: Bioconductor@r-project.org
> > Date: Wednesday, August 28, 2013, 2:44 PM
> >
> > Hi Oleg,
> > I just update pathview package so it can process and analyze
> > data labeled with KEGG gene IDs other than Entrez Gene. It
> > turns out that this issue affects many other species too. So
> > with this update, you can literaully work with all ~2300
> > (and more forth-coming) KEGG species data with pathview now.
> > I’ve also added new content with working examples on KEGG
> > species and Gene ID usage in page 14-16 of the vignette.
> > Notice that you need to specified gene.idtype="KEGG" when
> > calling pathview.
> > I’ve posted the new package to R-forge. You should be able
> > to access it in the next few hours at
> http://r-forge.r-project.org/R/?group_id=1619. Just
> > install it follow the instruction there. The Bioc version
> > will also be updated in the next 1-2 days:
> http://bioconductor.org/packages/devel/bioc/html/pathview.html.
> > Let me know how that works or if you have questions. HTH.
> > Weijun
> >
> > --------------------------------------------
> > On Fri, 8/23/13, Luo Weijun <luo_weijun@yahoo.com>
> > wrote:
> >
> > Subject: Re: [BioC] pathview puzzle
> > To: Bioconductor@r-project.org,
> > "Oleg Moskvin" <moskvin@wisc.edu>
> > Date: Friday, August 23, 2013, 9:53 PM
> >
> > Hi Oleg,
> > Thanks for the note. This is indeed a problem I didn’t
> > realize previously! KEGG uses Entrez Gene ID for all other
> > model organisms I’ve checked.
> > I am working on a generic fix (not only for E coli but
> > other
> > species with similar situation) and will incorporate that
> > into the development version of pathview soon. Will keep
> > you
> > posted.
> > Thanks for pointing this out.
> > Weijun
> >
> >
> > --------------------------------------------
> > On Fri, 8/23/13, Oleg Moskvin <moskvin@wisc.edu>
> > wrote:
> >
> > Subject: Re: [BioC] pathview puzzle
> > To: Bioconductor@r-project.org,
> > luo_weijun@yahoo.com
> > Date: Friday, August 23, 2013, 12:19 PM
> >
> > Hi Weijun,
> >
> > Thank you for the response.
> >
> > The problem seems to be deeper than that and is
> > connected
> > to
> > special handling of a particular species - E.coli -
> > by
> > KEGG.
> >
> >
> > I looked into the pathview() code and here is what I
> > see:
> >
> > 1) gene.data is remapped internally via mol.sum() to
> > have
> > ENTREZ IDs;
> > 2) remapped gene.data is used by node.map() to map
> > onto
> > KEGG
> > nodes using node.data
> > 3) the node.data used in (2) was originally extracted
> > from
> > the KEGG XML by node.info()
> >
> > The above route implies that the "name" entries in
> > the
> > KEGG
> > XML of type="gene" have "speciesID:ENTREZ" format...
> >
> > And in the case of E.coli this doesn't hold true! See
> > the
> > examples of XML entries for H.sapience and E.coli
> > from my
> > yesterday's message (below).
> >
> > In fact, in KEGG XML for E.coli "gene" records
> > b-numbers
> > are
> > used as IDs!
> >
> > So, for the cases like that, when KEGG fails to be
> > consistent in the supplied XML structure, one may
> > suggest
> > introducing an "id.bypass" option to pathview() which
> > will
> > take the gene.data as is (with the IDs supplied by
> > user
> > that
> > match KEGG XML ids; for example, b-numbers), and pass
> > this
> > directly to the step 3 (node matching).
> >
> > Thanks!
> >
> > Oleg
> >
> >
> >
> > On 08/22/13, Luo Weijun wrote:
> > > Hi Oleg,
> > > You are right, the problem is due to ID type
> > inconsistency.
> > > You have to specify gene.idtype when calling
> > pathview
> > function, if your gene id type is not Entrez Gene. I
> > don’t
> > think b-numbers are recognized for sure. For your
> > gene
> > name
> > example, if you mean official gene symbols by
> > “gene
> > name”, you should specify gene.idtype="SYMBOL"
> > (lower
> > case
> > is fine):
> > > eco2.out <- pathview(gene.data =
> > T2.CEBF095.crt115.ASCH.DROP3.rel.gn, pathway.id =
> > "02010",
> > gene.idtype="SYMBOL", out.suffix = "T2ACSH", species
> > =
> > "eco", kegg.native=TRUE)
> >
> >
> > On 08/22/13, Oleg Moskvin wrote:
> >
> > >
> > > <entry id="2" name="hsa:51343" type="gene"
> > > link="http://www.kegg.jp/dbget-bin/www_bget?hsa:51343">
> > > <graphics name="FZR1, CDC20C, CDH1, FZR,
> > FZR2,
> > HCDH,
> > HCDH1" fgcolor="#000000" bgcolor="#BFFFBF"
> > > type="rectangle" x="919" y="536" width="46"
> > height="17"/>
> > > </entry>
> > >
> > >
> > > <entry id="4" name="eco:b1513" type="gene"
> > > link="http://www.kegg.jp/dbget-bin/www_bget?eco:b1513">
> > > <graphics name="lsrA" fgcolor="#000000"
> > bgcolor="#BFFFBF"
> > > type="rectangle" x="339" y="1882" width="46"
> > height="17"/>
> > > </entry>
>
> --
> ---------------------------------------------------------
> Oleg Moskvin, PhD
> Associate Scientist (Computational Biology)
> Great Lakes Bioenergy Research Center
> University of Wisconsin-Madison
> 1552 University Ave Room 4241
> Madison, Wisconsin 53706
> Phone: (608) 890-2361
> Email: moskvin@wisc.edu
>
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