Dear All, How to create annotation package for not a supported (please see for available ones below) organism (e.g. D.magna: http://en.wikipedia.org/wiki/Daphnia_magna and other Crustaceans that are so important in environmental ecotoxicology/toxicogenomics)? What I have is a B2G annotation for probes arrayed on Agi4x44 chips. As I know Biocore Data Team is responsible for the annotation packages. But how do the select organism to support? Thanks Alex References: http://www.bioconductor.org/packages/2.6/bioc/vignettes/AnnotationDbi/ inst/doc/SQLForge.pdf http://www.bioconductor.org/packages/release/bioc/vignettes/Annotation Dbi/inst/doc/NewSchema.pdf >available.db0pkgs() [1] "anopheles.db0" "arabidopsis.db0" "bovine.db0" "canine.db0" "chicken.db0" "chimp.db0" "ecoliK12.db0" "ecoliSakai.db0" [9] "fly.db0" "human.db0" "malaria.db0" "mouse.db0" "pig.db0" "rat.db0" "rhesus.db0" "worm.db0" [17] "xenopus.db0" "yeast.db0" "zebrafish.db0" > sessionInfo() R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] hgug4112a.db_2.5.0 org.Hs.eg.db_2.5.0 affycoretools_1.24.0 KEGG.db_2.5.0 GO.db_2.5.0 RSQLite_0.9-4 [7] DBI_0.2-5 affy_1.30.0 gplots_2.10.1 KernSmooth_2.23-6 caTools_1.12 bitops_1.0-4.1 [13] gdata_2.8.2 gtools_2.6.2 marray_1.30.0 vsn_3.20.0 Agi4x44PreProcess_1.12.0 genefilter_1.34.0 [19] annotate_1.30.1 AnnotationDbi_1.14.1 limma_3.8.3 Biobase_2.12.2 loaded via a namespace (and not attached): [1] affyio_1.20.0 annaffy_1.24.0 biomaRt_2.8.1 Biostrings_2.20.3 Category_2.18.0 gcrma_2.24.1 [7] GOstats_2.18.0 graph_1.30.0 GSEABase_1.14.0 IRanges_1.10.6 lattice_0.19-30 preprocessCore_1.14.0 [13] RBGL_1.28.0 RCurl_1.6-10.1 splines_2.13.1 survival_2.36-9 tools_2.13.1 XML_3.4-2.2 [19] xtable_1.5-6 [[alternative HTML version deleted]]

Hi Alex, The Bioconductor package AnnotationDbi can be used to create new probe packages. A vignette outlining the process can be found at http://bioconductor.org/packages/2.9/bioc/html/AnnotationDbi.html We welcome new packages for unsupported organisms. When your package is ready you can submit it to us for inclusion in the next BioC release. I'm cc'ing Marc who is our primary contact for annotation packages. Valerie On 09/09/11 15:36, alogmail2 at aol.com wrote: > > > > > Dear All, > > How to create annotation package for not a supported (please see for available ones below) organism (e.g. D.magna: http://en.wikipedia.org/wiki/Daphnia_magna and other Crustaceans that are so important in environmental ecotoxicology/toxicogenomics)? > > What I have is a B2G annotation for probes arrayed on Agi4x44 chips. > > As I know Biocore Data Team is responsible for the annotation packages. But how do the select organism to support? > > > Thanks > > Alex > > > References: > http://www.bioconductor.org/packages/2.6/bioc/vignettes/AnnotationDb i/inst/doc/SQLForge.pdf > http://www.bioconductor.org/packages/release/bioc/vignettes/Annotati onDbi/inst/doc/NewSchema.pdf > > > > > > >available.db0pkgs() > [1] "anopheles.db0" "arabidopsis.db0" "bovine.db0" "canine.db0" "chicken.db0" "chimp.db0" "ecoliK12.db0" "ecoliSakai.db0" > [9] "fly.db0" "human.db0" "malaria.db0" "mouse.db0" "pig.db0" "rat.db0" "rhesus.db0" "worm.db0" > [17] "xenopus.db0" "yeast.db0" "zebrafish.db0" > > >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgug4112a.db_2.5.0 org.Hs.eg.db_2.5.0 affycoretools_1.24.0 KEGG.db_2.5.0 GO.db_2.5.0 RSQLite_0.9-4 > [7] DBI_0.2-5 affy_1.30.0 gplots_2.10.1 KernSmooth_2.23-6 caTools_1.12 bitops_1.0-4.1 > [13] gdata_2.8.2 gtools_2.6.2 marray_1.30.0 vsn_3.20.0 Agi4x44PreProcess_1.12.0 genefilter_1.34.0 > [19] annotate_1.30.1 AnnotationDbi_1.14.1 limma_3.8.3 Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 annaffy_1.24.0 biomaRt_2.8.1 Biostrings_2.20.3 Category_2.18.0 gcrma_2.24.1 > [7] GOstats_2.18.0 graph_1.30.0 GSEABase_1.14.0 IRanges_1.10.6 lattice_0.19-30 preprocessCore_1.14.0 > [13] RBGL_1.28.0 RCurl_1.6-10.1 splines_2.13.1 survival_2.36-9 tools_2.13.1 XML_3.4-2.2 > [19] xtable_1.5-6 > > > > > > > > > [[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