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Retrieving SRA files using Taxonomic IDs

I have a list of taxonomic IDs with genomic IDs as shown below:

Taxon ID Genome ID
1438833 1438833.3
1438845 1438845.3
1438847 1438847.3

Is there a way to retrieve SRA files using the above mentioned taxon IDs or Genome IDs??

eutility sra taxonomy
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written by Paul Paul

2 answers

I got my answer by doing this $ esearch -db sra -query "txid1448409[Organism:noexp]" | efetch -format runinfo | cut -d ',' -f 1 | grep SRR

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updated by GenoMax GenoMax • written by Paul Paul

using ncbi elink:

$ for F in 1438833 1438845 1438847 ; do curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=taxonomy&db=sra&id=${F}&retmode=xml"  ; done

https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20101123/elink.dtd">
<eLinkResult>

  <LinkSet>
    <DbFrom>taxonomy</DbFrom>
    <IdList>
      <Id>1438833</Id>
    </IdList>
    <LinkSetDb>
      <DbTo>sra</DbTo>
      <LinkName>taxonomy_sra</LinkName>

        <Link>
                <Id>648682</Id>
            </Link>

    </LinkSetDb>
    <LinkSetDb>
      <DbTo>sra</DbTo>
      <LinkName>taxonomy_sra_exp</LinkName>

        <Link>
                <Id>1438833</Id>
            </Link>
(...)
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks. So, the xmls need to get parsed for taxonomy_sra IDs??

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written by Paul Paul

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