[BioC] AnnBuilder and Kegg
John Zhang
jzhang at jimmy.harvard.edu
Wed Nov 22 14:25:08 CET 2006
>thank you for the suggestions.
>However, I downloaded the newest version of AnnBuilder
>and still I had the same problem in kegg connection.
Have you looked at the built package to see if you get any pathway annotation.
The warning messages like:
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00010.gene
just tell you that there are name miss-match in KEGG's data files but the data
package should still build.
I will try to write more informative warning messages when I get the chance.
>
>*******************************************************************************
***********************************
>
>sessionInfo()
>Version 2.3.1 (2006-06-01)
>i386-pc-linux-gnu
>
>attached base packages:
>[1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
>[7] "datasets" "base"
>
>other attached packages:
> GO AnnBuilder RSQLite DBI annotate XML
>Biobase
> "1.12.0" "1.12.0" "0.4-1" "0.1-10" "1.10.0" "0.99-7"
>"1.10.0"
>
>mySrcUrls <- c(GO=
>"http://www.godatabase.org/dev/database/archive/latest/go_2
>00605-termdb.rdf-xml.gz",KEGG="ftp://ftp.genome.ad.jp/pub/kegg/pathways",YG="ft
p
://genome-ftp.stanford.edu/pub/yeast/data_download/",HG="ftp://ftp.ncbi.nih.gov/
pub/HomoloGene/old/hmlg.ftp",EG="ftp://ftp.ncbi.nlm.nih.gov/gene/DATA",IPI="ftp:
//ftp.ebi.ac.uk/pub/databases/IPI/current/",YEAST="ftp://ftp.yeastgenome.org/pub
/yeast/sequence_similarity/domains/",KEGGGENOME="ftp://ftp.genome.ad.jp/pub/kegg
/tarfiles/genome",PFAM="ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_releas
e/Pfam-A.full.gz")
>ppbase<- file.path(.path.package("AnnBuilder"), "data",
>"lgtc.ids.1.txt")
>myBaseType="gb"
>ABPkgBuilder(baseName=ppbase,
>+ srcUrls = mySrcUrls,
>+ baseMapType = myBaseType,
>+ pkgName = "lgtc.221106",
>+ pkgPath = '.',
>+ organism ="mouse",
>+ version ="1.1.0",
>+ author = list(author = "Paola Pedotti",
>+ maintener ="Paola Pedotti <p.pedotti at lumc.nl>")
>+ )
>
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00010.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00020.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00030.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00031.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00040.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00051.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00052.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00053.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00061.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00062.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00071.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00072.gene
>Failed to get data from URL:
>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00100.gene
>......................
>
>
>*******************************************************************************
****************************
>
>
>Do you have other suggestions?
>
>thanks
>
>Paola
>
>
>On Tue, 2006-11-21 at 12:13 -0500, John Zhang wrote:
>> >
>> >Hi everybody,
>> >I am trying to annotate my dataset (home spotted array, two colors,
>> >mice) using AnnBuilder.
>> >Every time I run the program the connection with the kegg
>> >website is not working, so I am able to build the annotation
>> >package but not for the kegg pathways. Does anybody know how to
>> >fix this problem or did anybody find a way to by pass it (like
>> >downloading a list of accession numbers and corresponding pathways)?
>> >here my script:
>>
>> I guess the best thing for you to do is to update your R and BioC packages.
The
>> released version of AnnBuilder is 1.12.0 while you have 1.10.0 on your
machine.
>>
>>
>>
>> >
>>
>*******************************************************************************
>> **********************
>> >
>> >library(AnnBuilder)
>> >#Loading required package: Biobase
>> >#Loading required package: tools
>> >#Welcome to Bioconductor
>> ># Vignettes contain introductory material. To view,
>> ># simply type: openVignette()
>> ># For details on reading vignettes, see
>> ># the openVignette help page.
>> >#Loading required package: annotate
>> >
>> >library(GO)
>> >
>> >sessionInfo()
>> >
>> >#Version 2.3.1 (2006-06-01)
>> >#i386-pc-linux-gnu
>> >#
>> >#attached base packages:
>> >#[1] "splines" "tools" "methods" "stats" "graphics"
>> >#"grDevices"
>> >#[7] "utils" "datasets" "base"
>> >#
>> >#other attached packages:
>> >#
>> ># globaltest vsn limma multtest
>> ># "4.2.0" "1.10.0" "2.7.3" "1.10.2"
>> ># survival affydata affy affyio
>> ># "2.20" "1.8.0" "1.10.0" "1.0.0"
>> ># KEGG GO AnnBuilder RSQLite
>> ># "1.12.0" "1.12.0" "1.10.0" "0.4-1"
>> ># DBI annotate XML Biobase
>> ># "0.1-10" "1.10.0" "0.99-7" "1.10.0"
>> >
>> >
>> >mySrcUrls <- getSrcUrl("all", organism="Mus Musclusus")
>> >
>> >base<- file.path(.path.package("AnnBuilder"), "data", "lgtc.ids.1.txt")
>> >
>> >myBaseType<- "gbNRef"
>> >ABPkgBuilder(baseName=base,
>> > srcUrls = mySrcUrls,
>> > baseMapType = myBaseType,
>> > pkgName = "lgtc201106",
>> > pkgPath = ".",
>> > organism ="Mus Musclusus",
>> > version ="1.1.0",
>> > author = list(author = "Paola Pedotti",
>> > maintener ="Paola Pedotti <p.pedotti at lumc.nl>")
>> > )
>> >
>> >
>> >#Failed to get data from URL:
>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07214.gene
>> >#Failed to get data from URL:
>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07215.gene
>> >#Failed to get data from URL:
>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07216.gene
>> >#Failed to get data from URL:
>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07217.gene
>> >#Failed to get data from URL:
>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07218.gene
>> >#[1] "0 2 2"
>> >#Warning message:
>> >#cannot open file
>> >'/usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd',
>> >reason 'No such file or directory'
>> >#The following data sets have been added to the database and will be
>> >removed:
>> ># [1] "./lgtc161106/data/lgtc161106ACCNUM.rda"
>> ># [2] "./lgtc161106/data/lgtc161106CHR.rda"
>> ># [3] "./lgtc161106/data/lgtc161106ENZYME.rda"
>> ># [4] "./lgtc161106/data/lgtc161106GENENAME.rda"
>> ># [5] "./lgtc161106/data/lgtc161106GO.1.rda"
>> ># [6] "./lgtc161106/data/lgtc161106GO2ALLPROBES.rda"
>> ># [7] "./lgtc161106/data/lgtc161106GO2PROBE.rda"
>> ># [8] "./lgtc161106/data/lgtc161106GO.rda"
>> ># [9] "./lgtc161106/data/lgtc161106LOCUSID.rda"
>> >#[10] "./lgtc161106/data/lgtc161106MAPCOUNTS.rda"
>> >#[11] "./lgtc161106/data/lgtc161106MAP.rda"
>> >#[12] "./lgtc161106/data/lgtc161106OMIM.rda"
>> >#[13] "./lgtc161106/data/lgtc161106ORGANISM.rda"
>> >#[14] "./lgtc161106/data/lgtc161106PATH.rda"
>> >#[15] "./lgtc161106/data/lgtc161106PMID2PROBE.rda"
>> >#[16] "./lgtc161106/data/lgtc161106PMID.rda"
>> >#[17] "./lgtc161106/data/lgtc161106QCDATA.rda"
>> >#[18] "./lgtc161106/data/lgtc161106QC.rda"
>> >#[19] "./lgtc161106/data/lgtc161106REFSEQ.rda"
>> >#[20] "./lgtc161106/data/lgtc161106SUMFUNC.rda"
>> >#[21] "./lgtc161106/data/lgtc161106SYMBOL.rda"
>> >#[22] "./lgtc161106/data/lgtc161106UNIGENE.rda"
>> >#Warning message:
>> >#Can't
>> >copy /usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd
>> >in: copyTemplates(repList, pattern, pkgName, pkgPath)
>> >
>>
>*******************************************************************************
>> **********************
>> >
>> >
>> >thank you in advance
>> >
>> >Paola
>> >
>> >
>> >
>> >_______________________________________
>> >Center for Human and Clinical Genetics
>> >Leiden University Medical Center
>> >Postzone: S-04-P, Postbus 9600
>> >2300 RC Leiden, The Netherlands
>> >Telephone: +31 71 526 9440
>> >Fax: +31 71 526 8285
>> >
>> >_______________________________________________
>> >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
>>
>> Jianhua Zhang
>> Department of Medical Oncology
>> Dana-Farber Cancer Institute
>> 44 Binney Street
>> Boston, MA 02115-6084
>>
>
>_______________________________________________
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
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