Hi all, I have say 100 data set names from GEO, and for each, I want to pull out a reference using Efetch.
so for example, for the list:
GDS5204 GDS520 GDS4925
The output should be:
GDS4925 D'Souza M, Zhu X, Frisina RD. Novel approach to select genes from RMA normalized microarray data using functional hearing tests in aging mice. J Neurosci Methods 2008 Jun 30;171(2):279-87. PMID: 18455804
GDS520 Blalock EM, Chen KC, Sharrow K, Herman JP et al. Gene microarrays in hippocampal aging: statistical profiling identifies novel processes correlated with cognitive impairment. J Neurosci 2003 May 1;23(9):3807-19. PMID: 12736351
GDS5204 Lu T, Aron L, Zullo J, Pan Y et al. REST and stress resistance in ageing and Alzheimer's disease. Nature 2014 Mar 27;507(7493):448-54. PMID: 24670762
I am trying to use an Efetch command:
esearch -db GDS -query "GDS5204[ACCN]" | efetch -format docsum | xtract -pattern DocumentSummary -element PubMedIds
The command "runs" (as in no error), but there's also no output at all. I've tried editing different parts of the above command but I still just get the same thing.
Would someone know how to edit the above command to get the output described above (i.e. full reference for a set of data sets)?