You can get the information through the merged tables:
> dbListTables(con)
[1] "gds" "gds_subset" "geoConvert"
[4] "geodb_column_desc" "gpl" "gse"
[7] "gse_gpl" "gse_gsm" "gsm"
[10] "metaInfo" "sMatrix"
> cdesc = dbReadTable(con, "geodb_column_desc")
> poten = grep("gani", cdesc[,2])
> cdesc[poten,]
TableName FieldName
26 gpl organism
49 gsm organism_ch1
57 gsm organism_ch2
77 gds platform_organism
80 gds sample_organism
Description
26 [Values separated by ';tab', if more than one] Organism(s)
49 organism(s) from which the biological material was derived
57 same contents as ch1
77 organism of the platform
80 organism of the samples
On Sun, Oct 15, 2017 at 2:29 AM, Bohdan Khomtchouk <khomtchouk...@gmail.com>
wrote:
> library(GEOmetadb)
>
> if(!file.exists('GEOmetadb.sqlite')) getSQLiteFile()
>
> con <- dbConnect(SQLite(),'GEOmetadb.sqlite')
>
>
> dbListFields(con,'gse')
>
> ## [1] "ID" "title"
> ## [3] "gse" "status"
> ## [5] "submission_date" "last_update_date"
> ## [7] "pubmed_id" "summary"
> ## [9] "type" "contributor"
> ## [11] "web_link" "overall_design"
> ## [13] "repeats" "repeats_sample_list"
> ## [15] "variable" "variable_description"
> ## [17] "contact" "supplementary_file"
>
>
> Clearly, there should also be an "Organism" metadata field, e.g.:
> https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4032
>
> Please advise.
>
> --
>
> Bohdan Khomtchouk, Ph.D.
>
> Postdoctoral Research Scholar, Gozani Lab
>
> Department of Biology, Stanford University
>
> Gilbert Building, Room 206
>
> 371 Serra Mall
>
> Stanford, CA 94305-5020
>
> https://profiles.stanford.edu/bohdan-khomtchouk
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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