Question: Exclude Replaced or Discontinued UIDs from an reutils.esearch operation
gravatar for RamRS
4 months ago by
Houston, TX
RamRS20k wrote:


I'm using reutils to programmatically query NCBI's Gene database. Sometimes, I get multiple matches for a search (duh) and this list of results includes entries that have been discontinued or replaced (as shown in the Status filter on the Web UI below)

NCBI Search's Status filter

My question is:

How can I add a filter to my esearch call (or to the search term), so the search is restricted to only live/Current items? I can filter once I get the results when I make an esummary call, but can I do it at the esearch level?

My query term is UNQ6494[Gene Name] AND Homo sapiens[ORGN], and the r command is esearch(term="UNQ6494[Gene Name] AND Homo sapiens[ORGN]", db="gene")

Thank you!

eutils esearch ncbi • 183 views
ADD COMMENTlink modified 4 months ago by genomax64k • written 4 months ago by RamRS20k
gravatar for genomax
4 months ago by
United States
genomax64k wrote:
$ esearch -db gene -query "UNQ6494[Gene Name] AND Homo sapiens[ORGN] AND ALIVE[PROP]"  | efetch -format acc

1. UNQ6494
uncharacterized LOC100129066 [Homo sapiens (human)]
Chromosome: 9; Location: 9q22.2
Annotation: Chromosome 9 NC_000009.12 (89639783..89719759)
ID: 100129066
ADD COMMENTlink modified 4 months ago • written 4 months ago by genomax64k

Wonderful! I was trying live[Status] but alive[Prop] it was! Thank you!

ADD REPLYlink written 4 months ago by RamRS20k
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