Specify Assembly for NCBI Entrez Query
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2
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7.6 years ago
paulparsons ▴ 140

Does anyone know if it is possible to specify which assembly to use when constructing a query for Entrez ?

For example, if I do such a query with EDirect:

esearch -db gene -query "brca1 [ALL]human[ORGN]" -sort "relevance" | \
efetch -format docsum | \
xtract -pattern DocumentSummary -element Name MapLocation Description OtherAliases Id \
  -block GenomicInfo -element ChrLoc ChrAccVer ChrStart ChrStop

the GenomicInfo that I get seems to be according to the GRCh38 assembly. The application that I'm developing needs to use the GRCh37 assembly, however.

Any help is much appreciated.

entrez ncbi • 3.8k views
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7.6 years ago
paulparsons ▴ 140

Actually, it turns out that this can be done. I wrote to NCBI and got a response.

The key is to look in the LocationHistType block for:

  • a specific annotation release (see here and here for some explanation of annotation releases). For example, GRCh37.p13 is coded by NCBI as Annotation Release 105.

  • the corresponding assembly accession, which is a RefSeq Assembly ID. For GRCh37.p13 it is GCF_000001405.25 (see here for more information).

The EDirect commands should look something like this:

   esearch -db gene -query "brca1 [ALL] AND human [ORGN]" | \
   efetch -format docsum | \
   xtract -pattern DocumentSummary \
     -element Name MapLocation Description OtherAliases Id ChrLoc \
     -block LocationHistType \
       -match "AnnotationRelease:105" -and "AssemblyAccVer:GCF_000001405.25" \
         -element ChrAccVer ChrStart ChrStop
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0
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That's very valuable to know. Thanks for sharing what you found out!

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Good to know. Technically, this is "retrieve everything and parse for version" rather than "query using version", but whatever works.

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Good point. In my case (although maybe not in all cases), the difference doesn't really matter, and I can get the information that I need. Cheers.

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7.6 years ago
Neilfws 49k

I don't have a reference or source, but I'm certain that EUtils uses the current build, with no option to use previous versions. This came up in a previous question previous question.

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ha, there are some interesting dependencies there that I have never considered before, anyone that relies on eutils is tied to the current release

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