Annotate list of GSMxxxx GEO sample IDs with matching source GSExxx dataset identifier?

Question

[lkobzik]

I have file of gene expression data produced by ARCHS4 which is a table of genes in rows and sample IDs (e.g., GSM1132717, GSM1132728, GSM1233280 etc.) There are ~8K columns since this was a download of all whole blood samples in ARCHS4.

I ask for advice/tools to batch process the list of sample IDs to find their source GSE dataset, e.g by manual search: GSM1132717 comes from GSE46579, GSM1233280 from GSE50957 etc....

Thanks

Answer 1

[GenoMax]

Using EntrezDirect:

$ esearch -db biosample -query  GSM1132717 | elink -target bioproject | efetch -format native -mode xml | xtract -pattern DocumentSummary -element ID
GSE46579

$ esearch -db biosample -query  GSM1233280 | elink -target bioproject | efetch -format native -mode xml | xtract -pattern DocumentSummary -element ID
GSE50957

Answer 2

[Ankit]

I tried to do similar things before with combination of esearch and efetch but can't recall the syntax. You can check this https://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html

Other possibility is using R Package: GEOquery