Question: esearch query does not return sorted results from NCBI EDirect
gravatar for ciclistadan
4.3 years ago by
United States
ciclistadan30 wrote:

I'm having trouble returning sorted results using the esearch tool from NCBI EDirect (v3.60). A quick search on their website shows good sorting by relevance for the search term "aurora" with top results "AURKA", "AURKB" from the gene database. When I use the eDirect esearch command line interface on rhel, the result cannot be sorted by relevance (sorting by "chromosome" or "name" seems to work fine). Any tips on where I may be going wrong, or if anyone can reproduce this bug, I'd appreciate the help.

$ esearch -db gene -query "aurora" -sort relevance | \
  efetch -format docsum | \
  xtract -pattern DocumentSummary -element Id Name Description | head

7157    TP53    tumor protein p53
1956    EGFR    epidermal growth factor receptor
22059   Trp53   transformation related protein 53
2099    ESR1    estrogen receptor 1
672     BRCA1   breast cancer 1
3091    HIF1A   hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)
4790    NFKB1   nuclear factor of kappa light polypeptide gene enhancer in B-cells 1
5243    ABCB1   ATP binding cassette subfamily B member 1
367     AR      androgen receptor
207     AKT1    v-akt murine thymoma viral oncogene homolog 1
ADD COMMENTlink modified 19 months ago by h.mon29k • written 4.3 years ago by ciclistadan30

This has been asked a while back, any solutions? I'm getting the same problem

ADD REPLYlink written 3.5 years ago by hwsamuel0
gravatar for h.mon
19 months ago by
h.mon29k wrote:

It seems the problem has been solved at some point. On a Debian system, with esearch / efetch / xtract version 7.40 (Debian package ncbi-entrez-direct 7.40.20170928+ds-1), the same command now returns:

113427319   LOC113427319    aurora kinase C-like
113421273   AURKAIP1    aurora kinase A interacting protein 1
113417573   AUNIP   aurora kinase A and ninein interacting protein
7157    TP53    tumor protein p53
113415888   BORA    bora, aurora kinase A activator
113410492   LOC113410492    aurora kinase C-like
113410400   AURKA   aurora kinase A
113401558   LOC113401558    aurora kinase B
113396318   LOC113396318    serine/threonine-protein kinase Aurora-2
1956    EGFR    epidermal growth factor receptor
ADD COMMENTlink written 19 months ago by h.mon29k
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