[Bioc-devel] GEOmetadb package is missing "Organism" metadata field in all GSE accession IDs

[Vincent Carey]

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 <khomtchoukmed at 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
>
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>
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