Question: Retrieve "Abstract" of SRP accession from SRA
0
gravatar for grant.hovhannisyan
5 weeks ago by
grant.hovhannisyan1.9k wrote:

From SRA, how can I retrieve the "abstract" information for each SRP project in a list SRP projects?

For example, for SRP241771 I need "RNAseq data for Candida glabrata strain BG2 under different conditions".

SRA-toolkit and SRA Selector do not seems to have this function to download "abstracts".

Thanks

sra • 95 views
ADD COMMENTlink modified 5 weeks ago by genomax78k • written 5 weeks ago by grant.hovhannisyan1.9k

You can try sra-explorer https://ewels.github.io/sra-explorer/ then save the desired datasets to cart, and then use Full Metadata the button to download what is available.

ADD REPLYlink written 5 weeks ago by ATpoint29k

the loading of metadata hangs for some reason. also it does not seem to have the abstract info there

ADD REPLYlink written 4 weeks ago by grant.hovhannisyan1.9k
3
gravatar for genomax
5 weeks ago by
genomax78k
United States
genomax78k wrote:

Using Entrezdirect :

$ esearch -db sra -query "SRP241771" | esummary -format native | xtract -pattern STUDY_ABSTRACT -element STUDY_ABSTRACT
RNAseq data for Candida glabrata strain BG2 under different conditions
RNAseq data for Candida glabrata strain BG2 under different conditions
ADD COMMENTlink written 5 weeks ago by genomax78k

Exactly what I need, thanks, accepted!

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by grant.hovhannisyan1.9k
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