Hi, I found the KEGGgraph package in the development repository. It sounds great. But it is not working. There are no edges in the graphs! What is wrong? > library(KEGGgraph) > tmp <- tempfile() > retrieveKGML('04110', organism="hsa", destfile=tmp, method="wget", quiet=FALSE) --08:58:59-- ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04110.xml => `/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869' Aufl?sen des Hostnamen ?ftp.genome.jp? 133.103.100.184 Verbindungsaufbau zu ftp.genome.jp|133.103.100.184|:21... verbunden. Anmelden als anonymous ... Angemeldet! ==> SYST ... fertig. ==> PWD ... fertig. ==> TYPE I ... fertig. ==> CWD /pub/kegg/xml/organisms/hsa ... fertig. ==> PASV ... fertig. ==> RETR hsa04110.xml ... fertig. L?nge: 27.902 (27K) (unma?geblich) 100%[==============================================================>] 27.902 29.55K/s 08:59:04 (29.51 KB/s) - ?/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869? gespeichert [27902] > file.rename(tmp, paste(tmp,".xml",sep="")) [1] TRUE > tmp <- paste(tmp,".xml",sep="") > kegg <- parseKGML2Graph(tmp, expandGenes=T, genesOnly=T ) Fehler in subGraphByNodeType(gR, "gene") : No 'gene' type found in the file, maybe it is a map file. Please try parsing the file with 'genesOnly=FALSE' > parseKGML(tmp) KEGG Pathway [ Title ]: Cell cycle [ Name ]: path:hsa04110 [ Organism ]: hsa [ Number ] :04110 [ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04110.gif [ Link ] :http://www.genome.jp/dbget-bin/show_pathway?hsa04110 ------------------------------------------------------------ Statistics: 99 node(s) 0 edge(s) 0 reaction(s) ------------------------------------------------------------ > > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-linux-gnu locale: LC_CTYPE=de_DE at euro;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_ DE.UTF-8;LC_MONETARY=C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDEN TIFICATION=C attached base packages: [1] splines grid tools stats graphics grDevices utils [8] datasets methods base other attached packages: [1] org.Hs.eg.db_2.2.6 KEGGgraph_0.8.16 XML_1.98-1 [4] hgu133acdf_2.3.0 vsn_3.8.0 limma_2.16.2 [7] lattice_0.17-15 GeneNet_1.2.3 fdrtool_1.2.5 [10] longitudinal_1.1.4 corpcor_1.5.2 genefilter_1.22.0 [13] survival_2.34-1 hgu133a.db_2.2.5 RSQLite_0.7-1 [16] DBI_0.2-4 AnnotationDbi_1.4.0 pcalg_0.1-7 [19] mnormt_1.3-2 ggm_1.0.2 Rgraphviz_1.20.0 [22] robustbase_0.4-5 graph_1.19.6 MASS_7.2-44 [25] affy_1.20.0 Biobase_2.2.0 loaded via a namespace (and not attached): [1] affyio_1.10.1 annotate_1.20.0 cluster_1.11.11 [4] preprocessCore_1.4.0 Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4497

Hi Markus and to all bioconductor users, Thank you for the feedback. I have contacted staffs at KEGG and confirmed that the error is caused by an inconsistent update of KGML files - their current version of XML files are missing 'reaction' items and not complete. Therefore we have to wait the KEGG to update their files again. I will post here by then. Thank you very much again for the report and sorry for the inconvenience. Best wishes, Jitao David Zhang 2009/4/17 Markus Schmidberger <schmidb@ibe.med.uni-muenchen.de> > Hi, > > I found the KEGGgraph package in the development repository. It sounds > great. But it is not working. There are no edges in the graphs! > What is wrong? > > > library(KEGGgraph) > > tmp <- tempfile() > > retrieveKGML('04110', organism="hsa", destfile=tmp, method="wget", > quiet=FALSE) > --08:58:59-- ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04110.xml > => `/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869' > Auflösen des Hostnamen »ftp.genome.jp«.... 133.103.100.184 > Verbindungsaufbau zu ftp.genome.jp|133.103.100.184|:21... verbunden. > Anmelden als anonymous ... Angemeldet! > ==> SYST ... fertig. ==> PWD ... fertig. > ==> TYPE I ... fertig. ==> CWD /pub/kegg/xml/organisms/hsa ... fertig. > ==> PASV ... fertig. ==> RETR hsa04110.xml ... fertig. > Länge: 27.902 (27K) (unmaßgeblich) > > 100%[==============================================================>] > 27.902 29.55K/s > 08:59:04 (29.51 KB/s) - »/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869« > gespeichert [27902] > > > file.rename(tmp, paste(tmp,".xml",sep="")) > [1] TRUE > > tmp <- paste(tmp,".xml",sep="") > > kegg <- parseKGML2Graph(tmp, expandGenes=T, genesOnly=T ) > Fehler in subGraphByNodeType(gR, "gene") : > No 'gene' type found in the file, maybe it is a map file. Please try > parsing the file with 'genesOnly=FALSE' > > > > parseKGML(tmp) > KEGG Pathway > [ Title ]: Cell cycle > [ Name ]: path:hsa04110 > [ Organism ]: hsa > [ Number ] :04110 > [ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04110.gif > [ Link ] :http://www.genome.jp/dbget-bin/show_pathway?hsa04110 > ------------------------------------------------------------ > Statistics: > 99 node(s) > 0 edge(s) > 0 reaction(s) > ------------------------------------------------------------ > > > > > sessionInfo() > R version 2.8.0 (2008-10-20) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=de_DE@euro > ;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY =C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C ;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] splines grid tools stats graphics grDevices utils [8] > datasets methods base > other attached packages: > [1] org.Hs.eg.db_2.2.6 KEGGgraph_0.8.16 XML_1.98-1 [4] > hgu133acdf_2.3.0 vsn_3.8.0 limma_2.16.2 [7] > lattice_0.17-15 GeneNet_1.2.3 fdrtool_1.2.5 [10] > longitudinal_1.1.4 corpcor_1.5.2 genefilter_1.22.0 [13] > survival_2.34-1 hgu133a.db_2.2.5 RSQLite_0.7-1 [16] DBI_0.2-4 > AnnotationDbi_1.4.0 pcalg_0.1-7 [19] mnormt_1.3-2 > ggm_1.0.2 Rgraphviz_1.20.0 [22] robustbase_0.4-5 graph_1.19.6 > MASS_7.2-44 [25] affy_1.20.0 Biobase_2.2.0 > loaded via a namespace (and not attached): > [1] affyio_1.10.1 annotate_1.20.0 cluster_1.11.11 [4] > preprocessCore_1.4.0 > > > > > Thanks > Markus > > > > -- > Dipl.-Tech. Math. Markus Schmidberger > > Ludwig-Maximilians-Universität München > IBE - Institut für medizinische Informationsverarbeitung, > Biometrie und Epidemiologie > Marchioninistr. 15, D-81377 Muenchen > URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at] > ibe.med.uni-muenchen.de > Tel: +49 (089) 7095 - 4497 > > _______________________________________________ > 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 > -- Cheers, David [[alternative HTML version deleted]]

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 By the way, in the extdata directory of KEGGgraph package, there are several valid KGML files for the demo of KEGGgraph package functionality. Before the issue is fixed by KEGG database, one could also use these files (data stand November 2008) kgmlFile <- system.file("extdata/hsa04110.xml", package="KEGGgraph") graph <- parseKGML2Graph(kgmlFile) Best wishes, David Jitao Zhang wrote: > Hi dear Markus, > > Thanks for your feedback. It seems that the error is caused by an > mistake in the update of KEGG database - their current version of XMLs > are not complete. Therefore for now I do not think it is a bug of KEGGgraph. > > I will write to the maintainer of KEGG database to suggest the problem > of the XMLs and will udpate you when it is okay again. > > Best wishes, > David > > Markus Schmidberger wrote: >> Hi, > >> I found the KEGGgraph package in the development repository. It sounds >> great. But it is not working. There are no edges in the graphs! >> What is wrong? > >>> library(KEGGgraph) >>> tmp <- tempfile() >>> retrieveKGML('04110', organism="hsa", destfile=tmp, method="wget", >> quiet=FALSE) >> --08:58:59-- ftp://ftp.genome.jp/pub/kegg/xml/organisms/hsa/hsa04110.xml >> => `/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869' >> Aufl?sen des Hostnamen ?ftp.genome.jp? 133.103.100.184 >> Verbindungsaufbau zu ftp.genome.jp|133.103.100.184|:21... verbunden. >> Anmelden als anonymous ... Angemeldet! >> ==> SYST ... fertig. ==> PWD ... fertig. >> ==> TYPE I ... fertig. ==> CWD /pub/kegg/xml/organisms/hsa ... fertig. >> ==> PASV ... fertig. ==> RETR hsa04110.xml ... fertig. >> L?nge: 27.902 (27K) (unma?geblich) > >> 100%[==============================================================>] >> 27.902 29.55K/s >> 08:59:04 (29.51 KB/s) - ?/tmp/3127.1.maxmem.q/Rtmpe1YxAS/file643c9869? >> gespeichert [27902] > >>> file.rename(tmp, paste(tmp,".xml",sep="")) >> [1] TRUE >>> tmp <- paste(tmp,".xml",sep="") >>> kegg <- parseKGML2Graph(tmp, expandGenes=T, genesOnly=T ) >> Fehler in subGraphByNodeType(gR, "gene") : >> No 'gene' type found in the file, maybe it is a map file. Please try >> parsing the file with 'genesOnly=FALSE' > > >>> parseKGML(tmp) >> KEGG Pathway >> [ Title ]: Cell cycle >> [ Name ]: path:hsa04110 >> [ Organism ]: hsa >> [ Number ] :04110 >> [ Image ] :http://www.genome.jp/kegg/pathway/hsa/hsa04110.gif >> [ Link ] :http://www.genome.jp/dbget-bin/show_pathway?hsa04110 >> ------------------------------------------------------------ >> Statistics: >> 99 node(s) >> 0 edge(s) >> 0 reaction(s) >> ------------------------------------------------------------ >>> sessionInfo() >> R version 2.8.0 (2008-10-20) >> x86_64-unknown-linux-gnu > >> locale: >> LC_CTYPE=de_DE at euro;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE= de_DE.UTF-8;LC_MONETARY=C;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE.UTF-8 ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_I DENTIFICATION=C > > >> attached base packages: >> [1] splines grid tools stats graphics grDevices utils >> [8] datasets methods base >> other attached packages: >> [1] org.Hs.eg.db_2.2.6 KEGGgraph_0.8.16 XML_1.98-1 [4] >> hgu133acdf_2.3.0 vsn_3.8.0 limma_2.16.2 [7] >> lattice_0.17-15 GeneNet_1.2.3 fdrtool_1.2.5 [10] >> longitudinal_1.1.4 corpcor_1.5.2 genefilter_1.22.0 [13] >> survival_2.34-1 hgu133a.db_2.2.5 RSQLite_0.7-1 [16] >> DBI_0.2-4 AnnotationDbi_1.4.0 pcalg_0.1-7 [19] >> mnormt_1.3-2 ggm_1.0.2 Rgraphviz_1.20.0 [22] >> robustbase_0.4-5 graph_1.19.6 MASS_7.2-44 [25] >> affy_1.20.0 Biobase_2.2.0 >> loaded via a namespace (and not attached): >> [1] affyio_1.10.1 annotate_1.20.0 cluster_1.11.11 [4] >> preprocessCore_1.4.0 > > > > >> Thanks >> Markus > > > > > - -- THINK BEFORE YOU PRINT: DO OUR ENVIRONMENT GOOD Jitao David Zhang Computational Biology/Bioinformatics Ph.D. Candidate Division of Molecular Genome Analysis, DKFZ Im Neuenheimer Feld 580, Heidelberg D-69120 Germany Tel: 49-(0)6221-424711 Calendar: http://www.google.com/calendar/embed?src=38m77vcknecr59sbpdj0vofndo%40 group.calendar.google.com -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iEYEARECAAYFAknoObEACgkQb+FFFSdYGiCSIACePZrc1URhfdiHQkZwFfzcmzre UBsAn1OCyfoU1pYg017J34GB0lyCekXC =dkhA -----END PGP SIGNATURE-----