[BioC] R: problem with the KEGGSOAP package

[Marc Carlson]

Hello everyone,

KEGGSOAP does indeed use the KEGG API, so as long as KEGG keeps their 
promise to have this remain exposed we will be able to keep using 
KEGGSOAP.   Also, the default example from the manual page still works

## Still works:
try(get.pathways.by.genes(c("eco:b0077", "eco:b0078")))

And that tells me that this should still work if your ID is both 1) 
valid and 2) actually used to represent something at KEGG.


   Marc




On 08/09/2011 06:40 AM, Lapointe, David wrote:
> I wondered about this. At the bottom of the announcement link, Minoru adds:
>
> "Thank you for your immediate responses to this plea. I would like to emphasize that the KEGG web services, including the KEGG API, will be unaffected by the new mechanism to be introduced on July 1, 2011. Our policy for the use of the KEGG web site will remain unchanged. The only change will be to FTP access. We have already introduced a "Download KGML" link for the KGML files that used to be available only by FTP, and will continue to improve the functionality of KEGG API. I would be very grateful if you could consider obtaining a KEGG FTP subscription as your contribution to the KEGG project."
>
> So does KEGGSOAP not use the API?
>
> David
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Manca Marco (PATH)
> Sent: Tuesday, August 09, 2011 9:31 AM
> To: Naharajan Lakshmanaperumal; bioconductor at r-project.org
> Subject: [BioC] R: problem with the KEGGSOAP package
>
> Dear Naha,
>
> I suppose it has to do with this announcement:
> http://www.genome.jp/kegg/docs/plea.html
>
> from which I extract the information most relevant to your query:
> "Starting on July 1, 2011 the KEGG FTP site for academic users will be transferred from GenomeNet at Kyoto University to NPO Bioinformatics Japan, and it will be available only to paid subscribers."
>
> All the best, Marco
>
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
>
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
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> Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Naharajan Lakshmanaperumal [lakshman at mpi-cbg.de]
> Inviato: martedì 9 agosto 2011 15.28
> A: bioconductor at r-project.org
> Oggetto: [BioC] problem with the KEGGSOAP package
>
> Hi,
>
> I was trying to retrieve pathway information for genes in Mycobacterium tuberculosis. But I get no pathway information, if try to query it by gene-id.
>
> pathways<- try(get.pathways.by.genes(c("mtu:Rv2702")))
> pathways
> character(0)
>
> Anybody has an idea why this happens?
>
> Thanks in advance,
> Naha
>
>
>
>
>
>
>
>
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