[BioC] How to create annotation package for not a supported organism

[Valerie Obenchain]

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/AnnotationDbi/inst/doc/SQLForge.pdf
> http://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationDbi/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