How to download metadata from the SRA?

Question

[jaynaythan]

Hi,

I am trying to download the accompanying metadata to a list of SRA runs.

I would specifically like this type of data: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRR5070677&go=go

which includes place of isolation and date of isolation and other such good metadata.

Following the advice on the sra website: https://www.ncbi.nlm.nih.gov/books/NBK242621/#_SRA_Download_Guid_BK_Downloading_metadat_

does not get this type of data.

However i cannot figure out how to do this. Even teh runinfo document on this web page does nto provide all the information contained in this table.

Could anyone point me in the right direction?

Answer 1

[James Ashmore]

You can access all sorts of metadata from the NCBI databases using their E-utilities software. In your case, try this command:

esearch -db sra -query SRR5070677 | efetch -format runinfo

This will fetch all the associated run information for your run accession. If you want to do a bulk download of metadata for all runs in the same project, then instead use the bioproject accession:

esearch -db sra -query PRJNA279196 | efetch -format runinfo

[jaynaythan]

Hi James

What version of E utilities are you using?

I am using 2.1 and this does not work for me.I am looking into why this might be!

[jaynaythan]

For example, i cannot also get this command to work, form the examples page: esearch -db pubmed -query "lycopene cyclase" | efetch -format abstract

https://www.ncbi.nlm.nih.gov/books/NBK179288/