Obtain full taxonomic hierarchy from multiple species names

Question

[fibar]

I have got assembled metagenomic contigs, with multiple annotations per contig. The species name assigned to each annotation varies within contigs. It is suspicious, I know, but they are generally species of the same family. Considering this is due to the known difficulty of assigning sequences to the species level:

Is it possible to get the full taxonomy (genus, family, order, class, phylum) for a list of species names? That would allow me to cluster annotations at a higher taxonomic rank.

Example: Bacteroides thetaiotaomicron belongs to (Phylum)Bacteroidetes;(Class)Bacteroidetes;(Order)Bacteroidales;(Family)Bacteroidaceae

Any additional comment or question is welcome!

Answer 1

[jhc]

Using ete-ncbiquery you could do something like:

$ ete ncbiquery --search 9606 'Canis familiaris' --info

# Taxid Sci.Name Rank Named Lineage Taxid Lineage 

9606 Homo sapiens species root,cellular organisms,Eukaryota,Opisthokonta,Metazoa,Eumetazoa,Bilateria,Deuterostomia,Chordata,Craniata,Vertebrata,Gnathostomata,Teleostomi,Euteleostomi,Sarcopterygii,Dipnotetrapodomorpha,Tetrapoda,Amniota,Mammalia,Theria,Eutheria,Boreoeutheria,Euarchontoglires,Primates,Haplorrhini,Simiiformes,Catarrhini,Hominoidea,Hominidae,Homininae,Homo,Homo sapiens 1,131567,2759,33154,33208,6072,33213,33511,7711,89593,7742,7776,117570,117571,8287,1338369,32523,32524,40674,32525,9347,1437010,314146,9443,376913,314293,9526,314295,9604,207598,9605,9606 

9615 Canis lupus familiaris subspecies root,cellular organisms,Eukaryota,Opisthokonta,Metazoa,Eumetazoa,Bilateria,Deuterostomia,Chordata,Craniata,Vertebrata,Gnathostomata,Teleostomi,Euteleostomi,Sarcopterygii,Dipnotetrapodomorpha,Tetrapoda,Amniota,Mammalia,Theria,Eutheria,Boreoeutheria,Laurasiatheria,Carnivora,Caniformia,Canidae,Canis,Canis lupus,Canis lupus familiaris 1,131567,2759,33154,33208,6072,33213,33511,7711,89593,7742,7776,117570,117571,8287,1338369,32523,32524,40674,32525,9347,1437010,314145,33554,379584,9608,9611,9612,9615

Search terms can be PIPEd from files:

cut -f1 species.txt | ete ncbiquery  --info

Answer 2

[piet]

The NCBI taxonomy database comprises such information. They call it the lineage of a taxon. You can query the taxonomy database with eutils and retrieve the results in XML format. (In this particular case the XML is quite well human readable).

wget 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=818&retype=xml' -O - | less

Please note, that every node in the taxonomy database has a rank like 'species', 'genus', 'order'.

[erwan.scaon]

If you want to focus on the main taxonomic ranks, i.e. superkingdom, kingdom, phylum, class, order, family, genus & species, you can do the following :

efetch -db taxonomy \
       -id 9606 \
       -format xml \
       | xtract -pattern Taxon \
                -tab '\n' -sep '\t' \
                -element TaxId,ScientificName \
                -division LineageEx \
                -group Taxon \
                -if Rank -equals superkingdom \
                -or Rank -equals kingdom \
                -or Rank -equals phylum \
                -or Rank -equals class \
                -or Rank -equals order \
                -or Rank -equals family \
                -or Rank -equals genus \
                -tab '\n' -sep '\t' \
                -element Rank,ScientificName

Which yields :

9606    Homo sapiens
superkingdom    Eukaryota
kingdom Metazoa
phylum  Chordata
class   Mammalia
order   Primates
family  Hominidae
genus   Homo

Ps : All the doc for xtract is here : https://dataguide.nlm.nih.gov/edirect/xtract.html

Answer 3

[Pierre Lindenbaum]

One-liner using xpath:

echo "Bacteroides thetaiotaomicron" | tr " " "+" | \
    while read TERM; do \
        (xmllint --format --xpath '/eSearchResult/IdList/Id[1]/text()' \
        "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=${TERM}" && echo ) | \
        while read ID; do xmllint --xpath \
            'concat(/TaxaSet/Taxon/LineageEx/Taxon[Rank/text() = \
                "genus"]/ScientificName/text(),"|",/TaxaSet/Taxon/LineageEx/Taxon[Rank/text() = \
                "class"]/ScientificName/text(),"|",/TaxaSet/Taxon/LineageEx/Taxon[Rank/text() = \
                "order"]/ScientificName/text(),"|",/TaxaSet/Taxon/LineageEx/Taxon[Rank/text() = \
                "family"]/ScientificName/text())' \
            --format "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${ID}" \
        && echo ; done; done

output:

Bacteroides|Bacteroidia|Bacteroidales|Bacteroidaceae

Answer 4

[5heikki]

Entrez direct:

esearch -db taxonomy -query "Homo sapiens[Scientific Name]" | efetch -format xml | xtract -element Lineage

cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo

[Alex Voronin]

Where can I download esearch, efetch and xtract?

[5heikki]

Documentation is here and ftp dir here.