Question: Gi Number To Taxid To Phylum Name
0
gravatar for hdy
5.4 years ago by
hdy100
United States
hdy100 wrote:

I have a bunch of fasta files from NCBI, and I know to use gi_taxid_nucl.dmp to change gi into taxid numbers. But how to turn the taxid I got into their corresponding phyla names?

ncbi • 3.0k views
ADD COMMENTlink modified 5.4 years ago by Pierre Lindenbaum116k • written 5.4 years ago by hdy100
0
gravatar for Pierre Lindenbaum
5.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

you can use the NBCI E-Utilities:

$ xmllint --xpath '/TaxaSet/Taxon/LineageEx/Taxon[Rank="phylum"]/ScientificName/text()'  "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=9606" 
Chordata

or join the data to the dump for the taxonomy database, but you' ll have to re-create the NCBI tree from those data.

ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.Z

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by Pierre Lindenbaum116k

I have downloaded the taxdump but after I unzip it, there are several files. I think the most useful ones would be names.dmp and nodes.dmp. But none of both have a one to one relationship of taxid and its related phylum.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by hdy100

oh, that was the phylum. I've updated my answer .

ADD REPLYlink written 5.4 years ago by Pierre Lindenbaum116k

Sorry, but I mean the second method you said "join the data to the dump for the taxonomy database". I have downloaded the file and unzipped it. But none of those files have direct relationships between taxid and phylum names.

ADD REPLYlink written 5.4 years ago by hdy100

As I said, you have to re-construct the tree; See Last Common Ancestor from NCBI Taxonomy using Java for a java example.

ADD REPLYlink written 5.4 years ago by Pierre Lindenbaum116k
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