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