Question: problem with the KEGGSOAP package
0
gravatar for Naharajan Lakshmanaperumal
7.9 years ago by
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 [[alternative HTML version deleted]]
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ADD COMMENTlink modified 7.9 years ago by Manca Marco PATH340 • written 7.9 years ago by Naharajan Lakshmanaperumal10
Answer: problem with the KEGGSOAP package
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gravatar for Manca Marco PATH
7.9 years ago by
Manca Marco PATH340 wrote:
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) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.H2.032, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Naharajan Lakshmanaperumal [lakshman at mpi-cbg.de] Inviato: marted? 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.9 years ago by Manca Marco PATH340
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@r-project.org [mailto:bioconductor- bounces@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) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.H2.032, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Naharajan Lakshmanaperumal [lakshman at mpi-cbg.de] Inviato: marted? 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at 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 at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.9 years ago by David Lapointe170
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) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.H2.032, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht > > E-mail: m.manca at maastrichtuniversity.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > ******************************************************************** ************************************************* > > This email and any files transmitted with it are confidential and solely for the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA > > ******************************************************************** ************************************************* > ________________________________________ > Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] per conto di Naharajan Lakshmanaperumal [lakshman at mpi-cbg.de] > Inviato: marted? 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 > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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 at 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.9 years ago by Marc Carlson7.2k
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