Question: How to retrieve direct children of a taxon through Entrez using taxon IDs
gravatar for zbwrnz
8 months ago by
United States
zbwrnz0 wrote:

I am trying to retrieve the direct children of a taxon from entrez. I can accomplish this easily if I use the taxon name, for example:[NXLV]&RetMax=1000&RetStart=0

This retrieves all taxa whose immediate parent is 'Bacteria'.

However, taxon names are ambiguous. In this case, 'Bacteria' can refer to either the domain or to a genus of walking sticks (e.g. taxon 629398 from the link above).

So rather than use the term 'Bacteria' in the search, I would like to use the taxon ID.

But I can't directly replace Bacteria with its taxon ID (2)[NXLV]&RetMax=1000&RetStart=0

Or use the 'txid2' convention (which I've seen a few places)[NXLV]&RetMax=1000&RetStart=0

I've tried using the UID tag in tandem with NXLV, but only one tag seems to be considered[UID:NXLV]&RetMax=1000&RetStart=0

Using taxon ID ought to be at least as straightforward as using taxon name. Am I missing something?

eutils entrez taxonomy • 370 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 8 months ago by zbwrnz0

how about using the taxdump file to get all the children of a given id ?


This file represents taxonomy nodes. The description for each node includes 
the following fields:

    tax_id                  -- node id in GenBank taxonomy database
    parent tax_id               -- parent node id in GenBank taxonomy database
ADD REPLYlink written 8 months ago by Pierre Lindenbaum111k

Thanks Pierre! I probably should have provided more context. I am currently helping out with an R package that uses entrez ( One restriction of this package (by design) is that it does not require downloading and building entire databases. We have a related package, taxizedb, that builds an SQLite database from the taxonomy dump. In this case, getting the direct children is a trivial SQL command.

So, for this project, I would like to get the children just through a simple REST interface, if possible.

ADD REPLYlink written 8 months ago by zbwrnz0
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