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Using entrez or similar to find number of draft or complete genomes are associated with an SRA

Hi all, I want to find a straightforward way to determine if a genome in the nuccore database has an associated SRA dataset.

Example: I read this genome announcement. To find out whether there is a SRA dataset associated with it, I need to go to its nuccore entry, then to the bioproject page, and then look at the "project data section" to see if there an included entry in SRA (in this case, there is not).

Is there a way to determine this with Entrez, e-utils, or similar?

sra next-gen ncbi entrez
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written by nickp60 • nickp60

1 answer

Contacted SRA; this was their response:

If a user has a nuccore accession number like “AWUT00000000.1”

They can construct a search like so: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&id=AWUT00000000.1&version=2.0

this will allow them to have access to the BioProject accession number which can be used to search SRA records like so: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term=PRJNA213258

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written by nickp60 • nickp60

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