Closed sharifX closed 3 years ago
OK. I think I figured it out. It seems I need
>all_the_links <- entrez_link(dbfrom='taxonomy', id=99802, db='all')
> all_the_links$links$taxonomy_gene
[1] "6446594" "6446593" "6446592" "6446591" "6446590" "6446589" "6446588"
[8] "6446587" "6446586" "6446585" "6446584" "6446583" "6446582" "6446581"
[15] "6446580" "6446579" "6446578" "6446577" "6446576" "6446575" "6446574"
[22] "6446573" "6446572" "6446571" "6446570" "6446569" "6446568" "6446567"
[29] "6446566" "6446565" "6446564" "6446563" "6446562" "6446561" "6446560"
[36] "6446559"
What is the difference between dbfrom='taxonomy' and dbfrom='gene'?
--sharif
Hi @sharifX , sorry for letting this issue sit idle for so long and well done discovering the issue yourself.
In entrez_link, dbfrom
is the database from which the provided IDs were gathered. So if you set dbfrom
to "taxonomy"
the NCBI assumes the IDs are from the taxonomy database.
Hello, I am new to R and also to NCBI database. I am trying out some simple searches to understand the package. I started with a simple search based on a name.
So far so good. Now I want to use this taxon id to see all the links in the database. I am not sure if this is the right query. Why do I get only one link?
If I start with a gene id, I get more links:
And from there I can find the taxon id.
How do I find a link to 6446572 from the taxon search.
thanks. --sharif