Question: (Closed) Retrieve Full Lineage From Taxon Id

6.2 years ago by

Sophie • 30

Sophie • 30 wrote:

Hi,

I have a list of NCBI taxon ids for which I would like to have both the full lineage and common name information. That is, say, for 9606, the desired output would look like as follows:

Lineage: root; cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo

Common name: human

I checked the NCBI taxonomy FTP to see whether there is a mapping database but I could not find any.

Any help with this one?

PS. I recall that I came across a solution to this problem at BioStar (using taxdump), but I could not find that thread.

Thank you

taxonomy identifiers • 4.0k views

ADD COMMENT • link •

modified 5.8 years ago • written 6.2 years ago by Sophie • 30

the question was http://biostar.stackexchange.com/questions/7348 . Please close your question if it answers your needs.

ADD REPLY • link written 6.2 years ago by Pierre Lindenbaum ♦ 95k

Thanks for the reply, Pierre. But #7348 is not the thread that I was referring to.

ADD REPLY • link written 6.2 years ago by Sophie • 30

Since you answered your own question, I'll close as "no longer relevant."

ADD REPLY • link written 6.2 years ago by Neilfws ♦ 47k

6.2 years ago by

Pierre Lindenbaum ♦ 95k

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 95k wrote:

You can use the following stylesheet and NCBI E-Fetch for taxonomy:


<xsl:stylesheet xmlns:xsl="&lt;a href=" <a="" href="http://www.w3.org/1999/XSL/Transform" rel="nofollow">http://www.w3.org/1999/XSL/Transform" "="" rel="nofollow">http://www.w3.org/1999/XSL/Transform'
        version='1.0'
        >
<xsl:output method="text"/>

<xsl:template match="/">
<xsl:for-each select="/TaxaSet/Taxon/Lineage"><xsl:value-of select="concat('Lineage:root; ',text())"/><xsl:text>
</xsl:text></xsl:for-each>
</xsl:template>

</xsl:stylesheet>

Example:

xsltproc --novalid stylesheet.xsl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=9606&retmode=xml"

Result:

Lineage:root; cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo

ADD COMMENT • link written 6.2 years ago by Pierre Lindenbaum ♦ 95k

Hi Pierre,

What would be the script for a file (test_taxids.txt) having a list of taxids through this xml sheet to obtain the full taxonomic information?

ADD REPLY • link modified 8 days ago • written 8 days ago by Promi • 10

run a loop https://stackoverflow.com/questions/1521462

ADD REPLY • link written 8 days ago by Pierre Lindenbaum ♦ 95k

6.2 years ago by

Sophie • 30

Sophie • 30 wrote:

Okay, I figured out a pretty decent solution - Bioconductor.

1) Install Bioconductor

2) Install the package called 'genomes', i.e., biocLite("genomes")

3) The function "taxid2names" (e.g., taxid2names('9606')) returns the species name and the lineage given a taxon id.

4) I wrote a short script to read through all the taxon ids, get the species names and the linage using taxid2names, and write them out to a text file.

infile <- read.table("input.txt") # where input.txt includes the list of ids
i <- 1
while (i < 506) { # 506 = # of taxa + 1 // Well, alternatively you can easily get the length of your id vector and use it instead
v1 <- a[i,1]
v2 <- taxid2names(v1)
write.table(v2, "output.txt", append=TRUE)
i <- i + 1
}

ADD COMMENT • link written 6.2 years ago by Sophie • 30

needed a little tweak, but i m only a beginnner

infile <-read.table("input_taxid.txt",header=FALSE,sep="n"); i<-1; while(i<1202){ tmp <-infile$V1[i]; fulltaxa<-taxid2names(tmp); write.table(fulltaxa,"output_taxid.txt",append=TRUE); i<-i+1; }

needed a little tweak, but i m only a beginnner

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