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Question: GEOmetadb package is missing "Organism" metadata field in all GSE accession IDs
1
gravatar for Bohdan Khomtchouk
5 weeks ago by
Stanford University
Bohdan Khomtchouk10 wrote:

Hello, I ran into a bug in GEOmetadb:


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

Clearly, there should also be an "Organism" metadata field, e.g.: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4032

Clearly, there should also be an "Organism" metadata field, e.g.: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4032

Clearly, there should also be an "Organism" metadata field, e.g.: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4032

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.  Thank you!

ADD COMMENTlink modified 5 weeks ago by Vincent J. Carey, Jr.6.2k • written 5 weeks ago by Bohdan Khomtchouk10
1
gravatar for Vincent J. Carey, Jr.
5 weeks ago by
United States
Vincent J. Carey, Jr.6.2k wrote:

This was cross-posted to bioc-devel.  The answer that I provided there was:

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 sample
ADD COMMENTlink modified 5 weeks ago by Sean Davis21k • written 5 weeks ago by Vincent J. Carey, Jr.6.2k
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