Basic functions

All ncbi-taxonomist commands have the following underlying structure:

ncbi-taxonomist <command> <options>

This section shows the basic usage of ncbi-taxonomist. More complex examples, inlcuding data extraction with jq can be found here.

The output is a single JSON object or XML tree per line for each queried taxid, name, or accessions. The examples show pretty printed single results for clarity only.

Collect

The collect command fetches taxa from the Entrez database. If Taxids or names sharing parts of the same lineage, these taxa are printed only once.

Output format

The output describes the collected taxa, one per line. A single taxon has the following structure, for example chimpanzee (tx9598):

{
 "taxid" : 9598,
 "rank" : "species",
 "parentid" : 9596,
 "name" : "Pan troglodytes",
 "names" :
 {
  "Pan troglodytes" : "scientific_name",
  "chimpanzee" : "GenbankCommonName"
 }
}

Collecting taxa for chimpanzee and human:

ncbi-taxonomist  collect -n chimpanzee human

JSON output

{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}
{"taxid":2759,"rank":"superkingdom","names":{"Eukaryota":"scientific_name"},"parentid":131567,"name":"Eukaryota"}
{"taxid":33154,"rank":"clade","names":{"Opisthokonta":"scientific_name"},"parentid":2759,"name":"Opisthokonta"}
{"taxid":33208,"rank":"kingdom","names":{"Metazoa":"scientific_name"},"parentid":33154,"name":"Metazoa"}
{"taxid":6072,"rank":"clade","names":{"Eumetazoa":"scientific_name"},"parentid":33208,"name":"Eumetazoa"}
{"taxid":33213,"rank":"clade","names":{"Bilateria":"scientific_name"},"parentid":6072,"name":"Bilateria"}
{"taxid":33511,"rank":"clade","names":{"Deuterostomia":"scientific_name"},"parentid":33213,"name":"Deuterostomia"}
{"taxid":7711,"rank":"phylum","names":{"Chordata":"scientific_name"},"parentid":33511,"name":"Chordata"}
{"taxid":89593,"rank":"subphylum","names":{"Craniata":"scientific_name"},"parentid":7711,"name":"Craniata"}
{"taxid":7742,"rank":"clade","names":{"Vertebrata":"scientific_name"},"parentid":89593,"name":"Vertebrata"}
{"taxid":7776,"rank":"clade","names":{"Gnathostomata":"scientific_name"},"parentid":7742,"name":"Gnathostomata"}
{"taxid":117570,"rank":"clade","names":{"Teleostomi":"scientific_name"},"parentid":7776,"name":"Teleostomi"}
{"taxid":117571,"rank":"clade","names":{"Euteleostomi":"scientific_name"},"parentid":117570,"name":"Euteleostomi"}
{"taxid":8287,"rank":"superclass","names":{"Sarcopterygii":"scientific_name"},"parentid":117571,"name":"Sarcopterygii"}
{"taxid":1338369,"rank":"clade","names":{"Dipnotetrapodomorpha":"scientific_name"},"parentid":8287,"name":"Dipnotetrapodomorpha"}
{"taxid":32523,"rank":"clade","names":{"Tetrapoda":"scientific_name"},"parentid":1338369,"name":"Tetrapoda"}
{"taxid":32524,"rank":"clade","names":{"Amniota":"scientific_name"},"parentid":32523,"name":"Amniota"}
{"taxid":40674,"rank":"class","names":{"Mammalia":"scientific_name"},"parentid":32524,"name":"Mammalia"}
{"taxid":32525,"rank":"clade","names":{"Theria":"scientific_name"},"parentid":40674,"name":"Theria"}
{"taxid":9347,"rank":"clade","names":{"Eutheria":"scientific_name"},"parentid":32525,"name":"Eutheria"}
{"taxid":1437010,"rank":"clade","names":{"Boreoeutheria":"scientific_name"},"parentid":9347,"name":"Boreoeutheria"}
{"taxid":314146,"rank":"superorder","names":{"Euarchontoglires":"scientific_name"},"parentid":1437010,"name":"Euarchontoglires"}
{"taxid":9443,"rank":"order","names":{"Primates":"scientific_name"},"parentid":314146,"name":"Primates"}
{"taxid":376913,"rank":"suborder","names":{"Haplorrhini":"scientific_name"},"parentid":9443,"name":"Haplorrhini"}
{"taxid":314293,"rank":"infraorder","names":{"Simiiformes":"scientific_name"},"parentid":376913,"name":"Simiiformes"}
{"taxid":9526,"rank":"parvorder","names":{"Catarrhini":"scientific_name"},"parentid":314293,"name":"Catarrhini"}
{"taxid":314295,"rank":"superfamily","names":{"Hominoidea":"scientific_name"},"parentid":9526,"name":"Hominoidea"}
{"taxid":9604,"rank":"family","names":{"Hominidae":"scientific_name"},"parentid":314295,"name":"Hominidae"}
{"taxid":207598,"rank":"subfamily","names":{"Homininae":"scientific_name"},"parentid":9604,"name":"Homininae"}
{"taxid":9605,"rank":"genus","names":{"Homo":"scientific_name"},"parentid":207598,"name":"Homo"}
{"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"}
{"taxid":9596,"rank":"genus","names":{"Pan":"scientific_name"},"parentid":207598,"name":"Pan"}
{"taxid":9598,"rank":"species","names":{"Pan troglodytes":"scientific_name","chimpanzee":"GenbankCommonName"},"parentid":9596,"name":"Pan troglodytes"}

XML output

<taxon><taxid>131567</taxid><rank>no rank</rank><name>cellular organisms</name><parentid>None</parentid><names><name type="scientific_name">cellular organisms</name></names></taxon>
<taxon><taxid>2759</taxid><rank>superkingdom</rank><name>Eukaryota</name><parentid>131567</parentid><names><name type="scientific_name">Eukaryota</name></names></taxon>
<taxon><taxid>33154</taxid><rank>clade</rank><name>Opisthokonta</name><parentid>2759</parentid><names><name type="scientific_name">Opisthokonta</name></names></taxon>
<taxon><taxid>33208</taxid><rank>kingdom</rank><name>Metazoa</name><parentid>33154</parentid><names><name type="scientific_name">Metazoa</name></names></taxon>
<taxon><taxid>6072</taxid><rank>clade</rank><name>Eumetazoa</name><parentid>33208</parentid><names><name type="scientific_name">Eumetazoa</name></names></taxon>
<taxon><taxid>33213</taxid><rank>clade</rank><name>Bilateria</name><parentid>6072</parentid><names><name type="scientific_name">Bilateria</name></names></taxon>
<taxon><taxid>33511</taxid><rank>clade</rank><name>Deuterostomia</name><parentid>33213</parentid><names><name type="scientific_name">Deuterostomia</name></names></taxon>
<taxon><taxid>7711</taxid><rank>phylum</rank><name>Chordata</name><parentid>33511</parentid><names><name type="scientific_name">Chordata</name></names></taxon>
<taxon><taxid>89593</taxid><rank>subphylum</rank><name>Craniata</name><parentid>7711</parentid><names><name type="scientific_name">Craniata</name></names></taxon>
<taxon><taxid>7742</taxid><rank>clade</rank><name>Vertebrata</name><parentid>89593</parentid><names><name type="scientific_name">Vertebrata</name></names></taxon>
<taxon><taxid>7776</taxid><rank>clade</rank><name>Gnathostomata</name><parentid>7742</parentid><names><name type="scientific_name">Gnathostomata</name></names></taxon>
<taxon><taxid>117570</taxid><rank>clade</rank><name>Teleostomi</name><parentid>7776</parentid><names><name type="scientific_name">Teleostomi</name></names></taxon>
<taxon><taxid>117571</taxid><rank>clade</rank><name>Euteleostomi</name><parentid>117570</parentid><names><name type="scientific_name">Euteleostomi</name></names></taxon>
<taxon><taxid>8287</taxid><rank>superclass</rank><name>Sarcopterygii</name><parentid>117571</parentid><names><name type="scientific_name">Sarcopterygii</name></names></taxon>
<taxon><taxid>1338369</taxid><rank>clade</rank><name>Dipnotetrapodomorpha</name><parentid>8287</parentid><names><name type="scientific_name">Dipnotetrapodomorpha</name></names></taxon>
<taxon><taxid>32523</taxid><rank>clade</rank><name>Tetrapoda</name><parentid>1338369</parentid><names><name type="scientific_name">Tetrapoda</name></names></taxon>
<taxon><taxid>32524</taxid><rank>clade</rank><name>Amniota</name><parentid>32523</parentid><names><name type="scientific_name">Amniota</name></names></taxon>
<taxon><taxid>40674</taxid><rank>class</rank><name>Mammalia</name><parentid>32524</parentid><names><name type="scientific_name">Mammalia</name></names></taxon>
<taxon><taxid>32525</taxid><rank>clade</rank><name>Theria</name><parentid>40674</parentid><names><name type="scientific_name">Theria</name></names></taxon>
<taxon><taxid>9347</taxid><rank>clade</rank><name>Eutheria</name><parentid>32525</parentid><names><name type="scientific_name">Eutheria</name></names></taxon>
<taxon><taxid>1437010</taxid><rank>clade</rank><name>Boreoeutheria</name><parentid>9347</parentid><names><name type="scientific_name">Boreoeutheria</name></names></taxon>
<taxon><taxid>314146</taxid><rank>superorder</rank><name>Euarchontoglires</name><parentid>1437010</parentid><names><name type="scientific_name">Euarchontoglires</name></names></taxon>
<taxon><taxid>9443</taxid><rank>order</rank><name>Primates</name><parentid>314146</parentid><names><name type="scientific_name">Primates</name></names></taxon>
<taxon><taxid>376913</taxid><rank>suborder</rank><name>Haplorrhini</name><parentid>9443</parentid><names><name type="scientific_name">Haplorrhini</name></names></taxon>
<taxon><taxid>314293</taxid><rank>infraorder</rank><name>Simiiformes</name><parentid>376913</parentid><names><name type="scientific_name">Simiiformes</name></names></taxon>
<taxon><taxid>9526</taxid><rank>parvorder</rank><name>Catarrhini</name><parentid>314293</parentid><names><name type="scientific_name">Catarrhini</name></names></taxon>
<taxon><taxid>314295</taxid><rank>superfamily</rank><name>Hominoidea</name><parentid>9526</parentid><names><name type="scientific_name">Hominoidea</name></names></taxon>
<taxon><taxid>9604</taxid><rank>family</rank><name>Hominidae</name><parentid>314295</parentid><names><name type="scientific_name">Hominidae</name></names></taxon>
<taxon><taxid>207598</taxid><rank>subfamily</rank><name>Homininae</name><parentid>9604</parentid><names><name type="scientific_name">Homininae</name></names></taxon>
<taxon><taxid>9605</taxid><rank>genus</rank><name>Homo</name><parentid>207598</parentid><names><name type="scientific_name">Homo</name></names></taxon>
<taxon><taxid>9606</taxid><rank>species</rank><name>Homo sapiens</name><parentid>9605</parentid><names><name type="scientific_name">Homo sapiens</name><name type="GenbankCommonName">human</name><name type="CommonName">man</name></names></taxon>
<taxon><taxid>9596</taxid><rank>genus</rank><name>Pan</name><parentid>207598</parentid><names><name type="scientific_name">Pan</name></names></taxon>
<taxon><taxid>9598</taxid><rank>species</rank><name>Pan troglodytes</name><parentid>9596</parentid><names><name type="scientific_name">Pan troglodytes</name><name type="GenbankCommonName">chimpanzee</name></names></taxon>

Map

The map command maps taxonomic information for taxids, names, and accessions. Without specifing the -edb argument, nucleotide Entrez database is assumed.

Taxids and names

Taxids and names can be mapped together. The taxids and names can be separated by commas and/or space. However, names containing space need to be encapsulated by '. For example:

$: ncbi-taxonomist map -t 562, 10508 -n man 'Influenza B virus (B/Acre/121609/2012)', chimpanzee

Mapping accession

The default database to map accessions is nucleotide. To map an accession form a different database, it has to be specified by the –entrezdb/-edb argument.

Supported access Entrez databases

Entrez database Example
assembly ncbi-taxonomist map -edb assembly -a ASM1001476v1 ViralProj177933
bioproject ncbi-taxonomist map -edb bioproject -a PRJNA604394
nucleotide

ncbi-taxonomist map -edb nucleotide -a MH510449.1

ncbi-taxonomist map -a MH510449.1
protein ncbi-taxonomist map -a YP_009345145 -edb protein

Note

Querying the following databases does not return the queried accession in the results. Therefore, results cannot identify which accession corresponds to which results if more than one are requested. To solve the one-to-one relationship, each of the accessions from these databases needs to be queried one-by-one and not as batch query. Future releases will try to implement such queries.
  • biosample
  • biosystems
  • cdd
  • dbvar
  • gap
  • gapplus
  • gene
  • genome
  • geoprofiles: using accessions like GDS6063 should work
  • proteinclusters: commontaxonomy attribute can be used as name
  • sra: Only XML results. Needs a dedicated parser

Output format

The result shows the used command, query, type of result, and the corresponding taxon.

JSON output

Single mapping result
  • Taxon:
{
  "mode" : "mapping",
  "query" : "Influenza B virus (B/Acre/121609/2012)",
  "cast" : "taxon",
  "parentid" : 11520,
  "name" : "Influenza B virus (B/Acre/121609/2012)",
  "taxon" :
  {
    "taxid" : 1334390,
    "rank" : "no rank",
    "names" :
    {
      "Influenza B virus (B/Acre/121609/2012)" : "scientific_name"
    }
  }
}
  • Accession:
{
  "mode" : "mapping",
  "query" : "ASM1001476v1",
  "cast" : "accs",
  "db":"assembly",
  "uid":5515991,
  "accession" :
  {
    "taxid" : 1962788,
    "accessions" :
    {
      "assemblyaccession" : "GCA_010014765.1",
      "lastmajorreleaseaccession" : "GCA_010014765.1",
      "assemblyname" : "ASM1001476v1"
    }
  }
}
Multiple mapping results
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{"mode":"mapping","query":"Influenza B virus (B/Acre/121609/2012)","cast":"taxon","taxon":{"taxid":1334390,"rank":"no rank","names":{"Influenza B virus (B/Acre/121609/2012)":"scientific_name"},"parentid":11520,"name":"Influenza B virus (B/Acre/121609/2012)"}}
{"mode":"mapping","query":"man","cast":"taxon","taxon":{"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"}}
{"mode":"mapping","query":"562","cast":"taxon","taxon":{"taxid":562,"rank":"species","names":{"Escherichia coli":"scientific_name","Bacillus coli":"Synonym","Bacterium coli":"Synonym","Bacterium coli commune":"Synonym","Enterococcus coli":"Synonym","E. coli":"CommonName","Escherichia sp. 3_2_53FAA":"Includes","Escherichia sp. MAR":"Includes","bacterium 10a":"Includes","bacterium E3":"Includes","Escherichia/Shigella coli":"EquivalentName","ATCC 11775":"type material","ATCC:11775":"type material","BCCM/LMG:2092":"type material","CCUG 24":"type material","CCUG 29300":"type material","CCUG:24":"type material","CCUG:29300":"type material","CIP 54.8":"type material","CIP:54.8":"type material","DSM 30083":"type material","DSM:30083":"type material","IAM 12119":"type material","IAM:12119":"type material","JCM 1649":"type material","JCM:1649":"type material","LMG 2092":"type material","LMG:2092":"type material","NBRC 102203":"type material","NBRC:102203":"type material","NCCB 54008":"type material","NCCB:54008":"type material","NCTC 9001":"type material","NCTC:9001":"type material","personal::U5/41":"type material","strain U5/41":"type material"},"parentid":561,"name":"Escherichia coli"}}
{"mode":"mapping","query":"ASM1001476v1","cast":"accs","accession":{"taxid":1962788,"accessions":{"assemblyaccession":"GCA_010014765.1","lastmajorreleaseaccession":"GCA_010014765.1","assemblyname":"ASM1001476v1"},"db":"assembly","uid":5515991}}
{"mode":"mapping","query":"PRJNA604394","cast":"accs","accession":{"taxid":573,"accessions":{"project_id":604394,"project_acc":"PRJNA604394","project_name":"Klebsiella pneumoniae strain:S01"},"db":"bioproject","uid":604394}}

XML output

Single mapping result
  • Taxon:
<mapping>
  <query cast="taxon">man</query>
  <taxon>
    <taxid>9606</taxid>
    <rank>species</rank>
    <name>Homo sapiens</name>
    <parentid>9605</parentid>
    <names>
      <name type="scientific_name">Homo sapiens</name>
      <name type="GenbankCommonName">human</name>
      <name type="CommonName">man</name>
    </names>
  </taxon>
</mapping>
  • Accession:
<mapping>
  <query cast="accession">ASM1001476v1</query>
  <accession>
    <taxid>1962788</taxid>
    <uid>5515991</uid>
    <database>assembly</database>
    <accessions>
      <assemblyaccession>GCA_010014765.1</assemblyaccession>
      <lastmajorreleaseaccession>GCA_010014765.1</lastmajorreleaseaccession>
      <assemblyname>ASM1001476v1</assemblyname>
    </accessions>
  </accession>
</mapping>
Multiple mapping results
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<mapping><query cast="taxon">Influenza B virus (B/Acre/121609/2012)</query><taxon><taxid>1334390</taxid><rank>no rank</rank><name>Influenza B virus (B/Acre/121609/2012)</name><parentid>11520</parentid><names><name type="scientific_name">Influenza B virus (B/Acre/121609/2012)</name></names></taxon></mapping>
<mapping><query cast="taxon">man</query><taxon><taxid>9606</taxid><rank>species</rank><name>Homo sapiens</name><parentid>9605</parentid><names><name type="scientific_name">Homo sapiens</name><name type="GenbankCommonName">human</name><name type="CommonName">man</name></names></taxon></mapping>
<mapping><query cast="taxon">562</query><taxon><taxid>562</taxid><rank>species</rank><name>Escherichia coli</name><parentid>561</parentid><names><name type="scientific_name">Escherichia coli</name><name type="Synonym">Bacillus coli</name><name type="Synonym">Bacterium coli</name><name type="Synonym">Bacterium coli commune</name><name type="Synonym">Enterococcus coli</name><name type="CommonName">E. coli</name><name type="Includes">Escherichia sp. 3_2_53FAA</name><name type="Includes">Escherichia sp. MAR</name><name type="Includes">bacterium 10a</name><name type="Includes">bacterium E3</name><name type="EquivalentName">Escherichia/Shigella coli</name><name type="type material">ATCC 11775</name><name type="type material">ATCC:11775</name><name type="type material">BCCM/LMG:2092</name><name type="type material">CCUG 24</name><name type="type material">CCUG 29300</name><name type="type material">CCUG:24</name><name type="type material">CCUG:29300</name><name type="type material">CIP 54.8</name><name type="type material">CIP:54.8</name><name type="type material">DSM 30083</name><name type="type material">DSM:30083</name><name type="type material">IAM 12119</name><name type="type material">IAM:12119</name><name type="type material">JCM 1649</name><name type="type material">JCM:1649</name><name type="type material">LMG 2092</name><name type="type material">LMG:2092</name><name type="type material">NBRC 102203</name><name type="type material">NBRC:102203</name><name type="type material">NCCB 54008</name><name type="type material">NCCB:54008</name><name type="type material">NCTC 9001</name><name type="type material">NCTC:9001</name><name type="type material">personal::U5/41</name><name type="type material">strain U5/41</name></names></taxon></mapping>
<mapping><query cast="accession">PRJNA604394</query><accession><taxid>573</taxid><uid>604394</uid><database>bioproject</database><accessions><project_id>604394</project_id><project_acc>PRJNA604394</project_acc><project_name>Klebsiella pneumoniae strain:S01</project_name></accessions></accession></mapping>
<mapping><query cast="accession">ASM1001476v1</query><accession><taxid>1962788</taxid><uid>5515991</uid><database>assembly</database><accessions><assemblyaccession>GCA_010014765.1</assemblyaccession><lastmajorreleaseaccession>GCA_010014765.1</lastmajorreleaseaccession><assemblyname>ASM1001476v1</assemblyname></accessions></accession></mapping>

Resolve

The resolve command resolve lineages. Names and taxid can be resolved directly, while accessions need a mapping step first.

Taxids and names

ncbi-taxonomist  resolve -n man -t 2

Accessions

$: ncbi-taxonomist map -a QZWG01000002.1 MG831203  | ncbi-taxonomist resolve -m

Output format

The result shows the used command, query, type of result, and the corresponding lineage. In case of queried names or taxids, the data for the taxon used as query is shown. For accessions, the queried accession data is shown.

JSON output

Single mapping result
{
  "mode" : "resolve",
  "query" : "man",
  "cast" : "taxon",
  "parentid" : 9605,
  "name":"Homo sapiens",
  "taxon" :
  {
    "taxid" : 9606,
    "rank" : "species",
    "names" :
    {
      "Homo sapiens" : "scientific_name",
      "human" : "GenbankCommonName",
      "man" : "CommonName"
    }
  },
  "lineage":
  [
    {"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"},
    {"taxid":9605,"rank":"genus","names":{"Homo":"scientific_name"},"parentid":207598,"name":"Homo"},
    {"taxid":207598,"rank":"subfamily","names":{"Homininae":"scientific_name"},"parentid":9604,"name":"Homininae"},
    {"taxid":9604,"rank":"family","names":{"Hominidae":"scientific_name"},"parentid":314295,"name":"Hominidae"},
    {"taxid":314295,"rank":"superfamily","names":{"Hominoidea":"scientific_name"},"parentid":9526,"name":"Hominoidea"},
    {"taxid":9526,"rank":"parvorder","names":{"Catarrhini":"scientific_name"},"parentid":314293,"name":"Catarrhini"},
    {"taxid":314293,"rank":"infraorder","names":{"Simiiformes":"scientific_name"},"parentid":376913,"name":"Simiiformes"},
    {"taxid":376913,"rank":"suborder","names":{"Haplorrhini":"scientific_name"},"parentid":9443,"name":"Haplorrhini"},
    {"taxid":9443,"rank":"order","names":{"Primates":"scientific_name"},"parentid":314146,"name":"Primates"},
    {"taxid":314146,"rank":"superorder","names":{"Euarchontoglires":"scientific_name"},"parentid":1437010,"name":"Euarchontoglires"},
    {"taxid":1437010,"rank":"clade","names":{"Boreoeutheria":"scientific_name"},"parentid":9347,"name":"Boreoeutheria"},
    {"taxid":9347,"rank":"clade","names":{"Eutheria":"scientific_name"},"parentid":32525,"name":"Eutheria"},
    {"taxid":32525,"rank":"clade","names":{"Theria":"scientific_name"},"parentid":40674,"name":"Theria"},
    {"taxid":40674,"rank":"class","names":{"Mammalia":"scientific_name"},"parentid":32524,"name":"Mammalia"},
    {"taxid":32524,"rank":"clade","names":{"Amniota":"scientific_name"},"parentid":32523,"name":"Amniota"},
    {"taxid":32523,"rank":"clade","names":{"Tetrapoda":"scientific_name"},"parentid":1338369,"name":"Tetrapoda"},
    {"taxid":1338369,"rank":"clade","names":{"Dipnotetrapodomorpha":"scientific_name"},"parentid":8287,"name":"Dipnotetrapodomorpha"},
    {"taxid":8287,"rank":"superclass","names":{"Sarcopterygii":"scientific_name"},"parentid":117571,"name":"Sarcopterygii"},
    {"taxid":117571,"rank":"clade","names":{"Euteleostomi":"scientific_name"},"parentid":117570,"name":"Euteleostomi"},
    {"taxid":117570,"rank":"clade","names":{"Teleostomi":"scientific_name"},"parentid":7776,"name":"Teleostomi"},
    {"taxid":7776,"rank":"clade","names":{"Gnathostomata":"scientific_name"},"parentid":7742,"name":"Gnathostomata"},
    {"taxid":7742,"rank":"clade","names":{"Vertebrata":"scientific_name"},"parentid":89593,"name":"Vertebrata"},
    {"taxid":89593,"rank":"subphylum","names":{"Craniata":"scientific_name"},"parentid":7711,"name":"Craniata"},
    {"taxid":7711,"rank":"phylum","names":{"Chordata":"scientific_name"},"parentid":33511,"name":"Chordata"},
    {"taxid":33511,"rank":"clade","names":{"Deuterostomia":"scientific_name"},"parentid":33213,"name":"Deuterostomia"},
    {"taxid":33213,"rank":"clade","names":{"Bilateria":"scientific_name"},"parentid":6072,"name":"Bilateria"},
    {"taxid":6072,"rank":"clade","names":{"Eumetazoa":"scientific_name"},"parentid":33208,"name":"Eumetazoa"},
    {"taxid":33208,"rank":"kingdom","names":{"Metazoa":"scientific_name"},"parentid":33154,"name":"Metazoa"},
    {"taxid":33154,"rank":"clade","names":{"Opisthokonta":"scientific_name"},"parentid":2759,"name":"Opisthokonta"},
    {"taxid":2759,"rank":"superkingdom","names":{"Eukaryota":"scientific_name"},"parentid":131567,"name":"Eukaryota"},
    {"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}
  ]
}
Multiple mapping results
{"mode":"resolve","query":"man","cast":"taxon","taxon":{"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"},"lineage":[{"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"},{"taxid":9605,"rank":"genus","names":{"Homo":"scientific_name"},"parentid":207598,"name":"Homo"},{"taxid":207598,"rank":"subfamily","names":{"Homininae":"scientific_name"},"parentid":9604,"name":"Homininae"},{"taxid":9604,"rank":"family","names":{"Hominidae":"scientific_name"},"parentid":314295,"name":"Hominidae"},{"taxid":314295,"rank":"superfamily","names":{"Hominoidea":"scientific_name"},"parentid":9526,"name":"Hominoidea"},{"taxid":9526,"rank":"parvorder","names":{"Catarrhini":"scientific_name"},"parentid":314293,"name":"Catarrhini"},{"taxid":314293,"rank":"infraorder","names":{"Simiiformes":"scientific_name"},"parentid":376913,"name":"Simiiformes"},{"taxid":376913,"rank":"suborder","names":{"Haplorrhini":"scientific_name"},"parentid":9443,"name":"Haplorrhini"},{"taxid":9443,"rank":"order","names":{"Primates":"scientific_name"},"parentid":314146,"name":"Primates"},{"taxid":314146,"rank":"superorder","names":{"Euarchontoglires":"scientific_name"},"parentid":1437010,"name":"Euarchontoglires"},{"taxid":1437010,"rank":"clade","names":{"Boreoeutheria":"scientific_name"},"parentid":9347,"name":"Boreoeutheria"},{"taxid":9347,"rank":"clade","names":{"Eutheria":"scientific_name"},"parentid":32525,"name":"Eutheria"},{"taxid":32525,"rank":"clade","names":{"Theria":"scientific_name"},"parentid":40674,"name":"Theria"},{"taxid":40674,"rank":"class","names":{"Mammalia":"scientific_name"},"parentid":32524,"name":"Mammalia"},{"taxid":32524,"rank":"clade","names":{"Amniota":"scientific_name"},"parentid":32523,"name":"Amniota"},{"taxid":32523,"rank":"clade","names":{"Tetrapoda":"scientific_name"},"parentid":1338369,"name":"Tetrapoda"},{"taxid":1338369,"rank":"clade","names":{"Dipnotetrapodomorpha":"scientific_name"},"parentid":8287,"name":"Dipnotetrapodomorpha"},{"taxid":8287,"rank":"superclass","names":{"Sarcopterygii":"scientific_name"},"parentid":117571,"name":"Sarcopterygii"},{"taxid":117571,"rank":"clade","names":{"Euteleostomi":"scientific_name"},"parentid":117570,"name":"Euteleostomi"},{"taxid":117570,"rank":"clade","names":{"Teleostomi":"scientific_name"},"parentid":7776,"name":"Teleostomi"},{"taxid":7776,"rank":"clade","names":{"Gnathostomata":"scientific_name"},"parentid":7742,"name":"Gnathostomata"},{"taxid":7742,"rank":"clade","names":{"Vertebrata":"scientific_name"},"parentid":89593,"name":"Vertebrata"},{"taxid":89593,"rank":"subphylum","names":{"Craniata":"scientific_name"},"parentid":7711,"name":"Craniata"},{"taxid":7711,"rank":"phylum","names":{"Chordata":"scientific_name"},"parentid":33511,"name":"Chordata"},{"taxid":33511,"rank":"clade","names":{"Deuterostomia":"scientific_name"},"parentid":33213,"name":"Deuterostomia"},{"taxid":33213,"rank":"clade","names":{"Bilateria":"scientific_name"},"parentid":6072,"name":"Bilateria"},{"taxid":6072,"rank":"clade","names":{"Eumetazoa":"scientific_name"},"parentid":33208,"name":"Eumetazoa"},{"taxid":33208,"rank":"kingdom","names":{"Metazoa":"scientific_name"},"parentid":33154,"name":"Metazoa"},{"taxid":33154,"rank":"clade","names":{"Opisthokonta":"scientific_name"},"parentid":2759,"name":"Opisthokonta"},{"taxid":2759,"rank":"superkingdom","names":{"Eukaryota":"scientific_name"},"parentid":131567,"name":"Eukaryota"},{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}]}
{"mode":"resolve","query":"2","cast":"taxon","taxon":{"taxid":2,"rank":"superkingdom","names":{"Bacteria":"scientific_name","eubacteria":"GenbankCommonName","bacteria":"BlastName","Monera":"Inpart","Procaryotae":"Inpart","Prokaryota":"Inpart","Prokaryotae":"Inpart","prokaryote":"Inpart","prokaryotes":"Inpart"},"parentid":131567,"name":"Bacteria"},"lineage":[{"taxid":2,"rank":"superkingdom","names":{"Bacteria":"scientific_name","eubacteria":"GenbankCommonName","bacteria":"BlastName","Monera":"Inpart","Procaryotae":"Inpart","Prokaryota":"Inpart","Prokaryotae":"Inpart","prokaryote":"Inpart","prokaryotes":"Inpart"},"parentid":131567,"name":"Bacteria"},{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}]}
{"mode":"resolve","query":"MG831203","cast":"accs","accs":{"taxid":198112,"accessions":{"accessionversion":"MG831203.1","caption":"MG831203","extra":"gi|1496532032|gb|MG831203.1|"},"db":"nucleotide","uid":1496532032},"lineage":[{"taxid":198112,"rank":"species","names":{"Deformed wing virus":"scientific_name","DWV":"GenbankAcronym"},"parentid":232799,"name":"Deformed wing virus"},{"taxid":232799,"rank":"genus","names":{"Iflavirus":"scientific_name"},"parentid":699189,"name":"Iflavirus"},{"taxid":699189,"rank":"family","names":{"Iflaviridae":"scientific_name"},"parentid":464095,"name":"Iflaviridae"},{"taxid":464095,"rank":"order","names":{"Picornavirales":"scientific_name"},"parentid":2732506,"name":"Picornavirales"},{"taxid":2732506,"rank":"class","names":{"Pisoniviricetes":"scientific_name"},"parentid":2732408,"name":"Pisoniviricetes"},{"taxid":2732408,"rank":"phylum","names":{"Pisuviricota":"scientific_name"},"parentid":2732396,"name":"Pisuviricota"},{"taxid":2732396,"rank":"kingdom","names":{"Orthornavirae":"scientific_name"},"parentid":2559587,"name":"Orthornavirae"},{"taxid":2559587,"rank":"clade","names":{"Riboviria":"scientific_name"},"parentid":10239,"name":"Riboviria"},{"taxid":10239,"rank":"superkingdom","names":{"Viruses":"scientific_name"},"parentid":null,"name":"Viruses"}]}

XML output

Single mapping result
<resolve>
<query value="MG831203" cast="accession">
  <accession>
    <taxid>198112</taxid>
    <uid>1496532032</uid>
    <database>nucleotide</database>
    <accessions>
      <accessionversion>MG831203.1</accessionversion>
      <caption>MG831203</caption>
      <extra>gi|1496532032|gb|MG831203.1|</extra>
    </accessions>
  </accession>
</query>
<lineage>
  <taxon>
    <taxid>198112</taxid>
    <rank>species</rank>
    <name>Deformed wing virus</name>
    <parentid>232799</parentid>
    <names>
      <name type="scientific_name">Deformed wing virus</name>
      <name type="GenbankAcronym">DWV</name>
    </names>
  </taxon>
  <taxon>
    <taxid>232799</taxid>
    <rank>genus</rank>
    <name>Iflavirus</name>
    <parentid>699189</parentid>
    <names>
      <name type="scientific_name">Iflavirus</name>
    </names>
  </taxon>
  <taxon>
    <taxid>699189</taxid>
    <rank>family</rank>
    <name>Iflaviridae</name>
    <parentid>464095</parentid>
    <names>
      <name type="scientific_name">Iflaviridae</name>
    </names>
  </taxon>
  <taxon>
    <taxid>464095</taxid>
    <rank>order</rank>
    <name>Picornavirales</name>
    <parentid>2732506</parentid>
    <names>
      <name type="scientific_name">Picornavirales</name>
    </names>
  </taxon>
  <taxon>
    <taxid>2732506</taxid>
    <rank>class</rank>
    <name>Pisoniviricetes</name>
    <parentid>2732408</parentid>
    <names>
      <name type="scientific_name">Pisoniviricetes</name>
    </names>
  </taxon>
  <taxon>
    <taxid>2732408</taxid>
    <rank>phylum</rank>
    <name>Pisuviricota</name>
    <parentid>2732396</parentid>
    <names>
      <name type="scientific_name">Pisuviricota</name>
    </names>
  </taxon>
  <taxon>
    <taxid>2732396</taxid>
    <rank>kingdom</rank>
    <name>Orthornavirae</name>
    <parentid>2559587</parentid>
    <names>
      <name type="scientific_name">Orthornavirae</name>
    </names>
  </taxon>
  <taxon>
    <taxid>2559587</taxid>
    <rank>clade</rank>
    <name>Riboviria</name>
    <parentid>10239</parentid>
    <names>
      <name type="scientific_name">Riboviria</name>
    </names>
  </taxon>
  <taxon>
    <taxid>10239</taxid>
    <rank>superkingdom</rank>
    <name>Viruses</name>
    <parentid>None</parentid>
    <names>
      <name type="scientific_name">Viruses</name>
    </names>
  </taxon>
</lineage>
</resolve>
Multiple mapping results
<resolve><query value="man" cast="name"><taxon><taxid>9606</taxid><rank>species</rank><name>Homo sapiens</name><parentid>9605</parentid><names><name type="scientific_name">Homo sapiens</name><name type="GenbankCommonName">human</name><name type="CommonName">man</name></names></taxon></query><lineage><taxon><taxid>9606</taxid><rank>species</rank><name>Homo sapiens</name><parentid>9605</parentid><names><name type="scientific_name">Homo sapiens</name><name type="GenbankCommonName">human</name><name type="CommonName">man</name></names></taxon><taxon><taxid>9605</taxid><rank>genus</rank><name>Homo</name><parentid>207598</parentid><names><name type="scientific_name">Homo</name></names></taxon><taxon><taxid>207598</taxid><rank>subfamily</rank><name>Homininae</name><parentid>9604</parentid><names><name type="scientific_name">Homininae</name></names></taxon><taxon><taxid>9604</taxid><rank>family</rank><name>Hominidae</name><parentid>314295</parentid><names><name type="scientific_name">Hominidae</name></names></taxon><taxon><taxid>314295</taxid><rank>superfamily</rank><name>Hominoidea</name><parentid>9526</parentid><names><name type="scientific_name">Hominoidea</name></names></taxon><taxon><taxid>9526</taxid><rank>parvorder</rank><name>Catarrhini</name><parentid>314293</parentid><names><name type="scientific_name">Catarrhini</name></names></taxon><taxon><taxid>314293</taxid><rank>infraorder</rank><name>Simiiformes</name><parentid>376913</parentid><names><name type="scientific_name">Simiiformes</name></names></taxon><taxon><taxid>376913</taxid><rank>suborder</rank><name>Haplorrhini</name><parentid>9443</parentid><names><name type="scientific_name">Haplorrhini</name></names></taxon><taxon><taxid>9443</taxid><rank>order</rank><name>Primates</name><parentid>314146</parentid><names><name type="scientific_name">Primates</name></names></taxon><taxon><taxid>314146</taxid><rank>superorder</rank><name>Euarchontoglires</name><parentid>1437010</parentid><names><name type="scientific_name">Euarchontoglires</name></names></taxon><taxon><taxid>1437010</taxid><rank>clade</rank><name>Boreoeutheria</name><parentid>9347</parentid><names><name type="scientific_name">Boreoeutheria</name></names></taxon><taxon><taxid>9347</taxid><rank>clade</rank><name>Eutheria</name><parentid>32525</parentid><names><name type="scientific_name">Eutheria</name></names></taxon><taxon><taxid>32525</taxid><rank>clade</rank><name>Theria</name><parentid>40674</parentid><names><name type="scientific_name">Theria</name></names></taxon><taxon><taxid>40674</taxid><rank>class</rank><name>Mammalia</name><parentid>32524</parentid><names><name type="scientific_name">Mammalia</name></names></taxon><taxon><taxid>32524</taxid><rank>clade</rank><name>Amniota</name><parentid>32523</parentid><names><name type="scientific_name">Amniota</name></names></taxon><taxon><taxid>32523</taxid><rank>clade</rank><name>Tetrapoda</name><parentid>1338369</parentid><names><name type="scientific_name">Tetrapoda</name></names></taxon><taxon><taxid>1338369</taxid><rank>clade</rank><name>Dipnotetrapodomorpha</name><parentid>8287</parentid><names><name type="scientific_name">Dipnotetrapodomorpha</name></names></taxon><taxon><taxid>8287</taxid><rank>superclass</rank><name>Sarcopterygii</name><parentid>117571</parentid><names><name type="scientific_name">Sarcopterygii</name></names></taxon><taxon><taxid>117571</taxid><rank>clade</rank><name>Euteleostomi</name><parentid>117570</parentid><names><name type="scientific_name">Euteleostomi</name></names></taxon><taxon><taxid>117570</taxid><rank>clade</rank><name>Teleostomi</name><parentid>7776</parentid><names><name type="scientific_name">Teleostomi</name></names></taxon><taxon><taxid>7776</taxid><rank>clade</rank><name>Gnathostomata</name><parentid>7742</parentid><names><name type="scientific_name">Gnathostomata</name></names></taxon><taxon><taxid>7742</taxid><rank>clade</rank><name>Vertebrata</name><parentid>89593</parentid><names><name type="scientific_name">Vertebrata</name></names></taxon><taxon><taxid>89593</taxid><rank>subphylum</rank><name>Craniata</name><parentid>7711</parentid><names><name type="scientific_name">Craniata</name></names></taxon><taxon><taxid>7711</taxid><rank>phylum</rank><name>Chordata</name><parentid>33511</parentid><names><name type="scientific_name">Chordata</name></names></taxon><taxon><taxid>33511</taxid><rank>clade</rank><name>Deuterostomia</name><parentid>33213</parentid><names><name type="scientific_name">Deuterostomia</name></names></taxon><taxon><taxid>33213</taxid><rank>clade</rank><name>Bilateria</name><parentid>6072</parentid><names><name type="scientific_name">Bilateria</name></names></taxon><taxon><taxid>6072</taxid><rank>clade</rank><name>Eumetazoa</name><parentid>33208</parentid><names><name type="scientific_name">Eumetazoa</name></names></taxon><taxon><taxid>33208</taxid><rank>kingdom</rank><name>Metazoa</name><parentid>33154</parentid><names><name type="scientific_name">Metazoa</name></names></taxon><taxon><taxid>33154</taxid><rank>clade</rank><name>Opisthokonta</name><parentid>2759</parentid><names><name type="scientific_name">Opisthokonta</name></names></taxon><taxon><taxid>2759</taxid><rank>superkingdom</rank><name>Eukaryota</name><parentid>131567</parentid><names><name type="scientific_name">Eukaryota</name></names></taxon><taxon><taxid>131567</taxid><rank>no rank</rank><name>cellular organisms</name><parentid>None</parentid><names><name type="scientific_name">cellular organisms</name></names></taxon></lineage></resolve>
<resolve><query value="2" cast="taxid"><taxon><taxid>2</taxid><rank>superkingdom</rank><name>Bacteria</name><parentid>131567</parentid><names><name type="scientific_name">Bacteria</name><name type="GenbankCommonName">eubacteria</name><name type="BlastName">bacteria</name><name type="Inpart">Monera</name><name type="Inpart">Procaryotae</name><name type="Inpart">Prokaryota</name><name type="Inpart">Prokaryotae</name><name type="Inpart">prokaryote</name><name type="Inpart">prokaryotes</name></names></taxon></query><lineage><taxon><taxid>2</taxid><rank>superkingdom</rank><name>Bacteria</name><parentid>131567</parentid><names><name type="scientific_name">Bacteria</name><name type="GenbankCommonName">eubacteria</name><name type="BlastName">bacteria</name><name type="Inpart">Monera</name><name type="Inpart">Procaryotae</name><name type="Inpart">Prokaryota</name><name type="Inpart">Prokaryotae</name><name type="Inpart">prokaryote</name><name type="Inpart">prokaryotes</name></names></taxon><taxon><taxid>131567</taxid><rank>no rank</rank><name>cellular organisms</name><parentid>None</parentid><names><name type="scientific_name">cellular organisms</name></names></taxon></lineage></resolve>
<resolve><query value="MG831203" cast="accession"><accession><taxid>198112</taxid><uid>1496532032</uid><database>nucleotide</database><accessions><accessionversion>MG831203.1</accessionversion><caption>MG831203</caption><extra>gi|1496532032|gb|MG831203.1|</extra></accessions></accession></query><lineage><taxon><taxid>198112</taxid><rank>species</rank><name>Deformed wing virus</name><parentid>232799</parentid><names><name type="scientific_name">Deformed wing virus</name><name type="GenbankAcronym">DWV</name></names></taxon><taxon><taxid>232799</taxid><rank>genus</rank><name>Iflavirus</name><parentid>699189</parentid><names><name type="scientific_name">Iflavirus</name></names></taxon><taxon><taxid>699189</taxid><rank>family</rank><name>Iflaviridae</name><parentid>464095</parentid><names><name type="scientific_name">Iflaviridae</name></names></taxon><taxon><taxid>464095</taxid><rank>order</rank><name>Picornavirales</name><parentid>2732506</parentid><names><name type="scientific_name">Picornavirales</name></names></taxon><taxon><taxid>2732506</taxid><rank>class</rank><name>Pisoniviricetes</name><parentid>2732408</parentid><names><name type="scientific_name">Pisoniviricetes</name></names></taxon><taxon><taxid>2732408</taxid><rank>phylum</rank><name>Pisuviricota</name><parentid>2732396</parentid><names><name type="scientific_name">Pisuviricota</name></names></taxon><taxon><taxid>2732396</taxid><rank>kingdom</rank><name>Orthornavirae</name><parentid>2559587</parentid><names><name type="scientific_name">Orthornavirae</name></names></taxon><taxon><taxid>2559587</taxid><rank>clade</rank><name>Riboviria</name><parentid>10239</parentid><names><name type="scientific_name">Riboviria</name></names></taxon><taxon><taxid>10239</taxid><rank>superkingdom</rank><name>Viruses</name><parentid>None</parentid><names><name type="scientific_name">Viruses</name></names></taxon></lineage></resolve>

Import

The import command import taxa, lineages, and accessions into a local SQLite database. The import command will print the resulkts from the preceding command to stanard output.

Local database schema

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CREATE TABLE taxa
              (id           INTEGER PRIMARY KEY,
               taxonid     INT NOT NULL,
               rank         TEXT NULL,
               parentid    INT NULL,
               UNIQUE(taxonid));
CREATE UNIQUE INDEX taxa_idx ON taxa (taxonid);
CREATE TABLE names
              (id           INTEGER PRIMARY KEY,
                taxonid     INT,
                name         TEXT,
                type         TEXT NULL,
                FOREIGN KEY (taxonid) REFERENCES taxa(taxonid) ON DELETE CASCADE,
                UNIQUE(taxonid, name));
CREATE TRIGGER delete_names DELETE ON names
              BEGIN DELETE FROM names WHERE taxonid=old.taxonid; END;
CREATE UNIQUE INDEX names_idx ON names (taxonid, name);
CREATE TABLE accessions
              (id        INTEGER PRIMARY KEY,
               accession TEXT NOT NULL,
               db        TEXT NOT NULL,
               type      TEXT NULL,
               uid       INT NOT NULL,
               taxonid  INT NOT NULL,
               FOREIGN KEY (taxonid) REFERENCES taxa(taxonid) ON DELETE CASCADE,
               UNIQUE(accession, uid));
CREATE TRIGGER delete_uids DELETE ON accessions
              BEGIN DELETE FROM accessions WHERE uid=old.uid; END;
CREATE UNIQUE INDEX accessions_idx ON
              accessions (accession, uid);

Import taxa via collect

ncbi-taxonomist  collect -n man -t 2 | ncbi-taxonomist --database taxa-collect.db
{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}
{"taxid":2759,"rank":"superkingdom","names":{"Eukaryota":"scientific_name"},"parentid":131567,"name":"Eukaryota"}
{"taxid":33154,"rank":"clade","names":{"Opisthokonta":"scientific_name"},"parentid":2759,"name":"Opisthokonta"}
{"taxid":33208,"rank":"kingdom","names":{"Metazoa":"scientific_name"},"parentid":33154,"name":"Metazoa"}
{"taxid":6072,"rank":"clade","names":{"Eumetazoa":"scientific_name"},"parentid":33208,"name":"Eumetazoa"}
{"taxid":33213,"rank":"clade","names":{"Bilateria":"scientific_name"},"parentid":6072,"name":"Bilateria"}
{"taxid":33511,"rank":"clade","names":{"Deuterostomia":"scientific_name"},"parentid":33213,"name":"Deuterostomia"}
{"taxid":7711,"rank":"phylum","names":{"Chordata":"scientific_name"},"parentid":33511,"name":"Chordata"}
{"taxid":89593,"rank":"subphylum","names":{"Craniata":"scientific_name"},"parentid":7711,"name":"Craniata"}
{"taxid":7742,"rank":"clade","names":{"Vertebrata":"scientific_name"},"parentid":89593,"name":"Vertebrata"}
{"taxid":7776,"rank":"clade","names":{"Gnathostomata":"scientific_name"},"parentid":7742,"name":"Gnathostomata"}
{"taxid":117570,"rank":"clade","names":{"Teleostomi":"scientific_name"},"parentid":7776,"name":"Teleostomi"}
{"taxid":117571,"rank":"clade","names":{"Euteleostomi":"scientific_name"},"parentid":117570,"name":"Euteleostomi"}
{"taxid":8287,"rank":"superclass","names":{"Sarcopterygii":"scientific_name"},"parentid":117571,"name":"Sarcopterygii"}
{"taxid":1338369,"rank":"clade","names":{"Dipnotetrapodomorpha":"scientific_name"},"parentid":8287,"name":"Dipnotetrapodomorpha"}
{"taxid":32523,"rank":"clade","names":{"Tetrapoda":"scientific_name"},"parentid":1338369,"name":"Tetrapoda"}
{"taxid":32524,"rank":"clade","names":{"Amniota":"scientific_name"},"parentid":32523,"name":"Amniota"}
{"taxid":40674,"rank":"class","names":{"Mammalia":"scientific_name"},"parentid":32524,"name":"Mammalia"}
{"taxid":32525,"rank":"clade","names":{"Theria":"scientific_name"},"parentid":40674,"name":"Theria"}
{"taxid":9347,"rank":"clade","names":{"Eutheria":"scientific_name"},"parentid":32525,"name":"Eutheria"}
{"taxid":1437010,"rank":"clade","names":{"Boreoeutheria":"scientific_name"},"parentid":9347,"name":"Boreoeutheria"}
{"taxid":314146,"rank":"superorder","names":{"Euarchontoglires":"scientific_name"},"parentid":1437010,"name":"Euarchontoglires"}
{"taxid":9443,"rank":"order","names":{"Primates":"scientific_name"},"parentid":314146,"name":"Primates"}
{"taxid":376913,"rank":"suborder","names":{"Haplorrhini":"scientific_name"},"parentid":9443,"name":"Haplorrhini"}
{"taxid":314293,"rank":"infraorder","names":{"Simiiformes":"scientific_name"},"parentid":376913,"name":"Simiiformes"}
{"taxid":9526,"rank":"parvorder","names":{"Catarrhini":"scientific_name"},"parentid":314293,"name":"Catarrhini"}
{"taxid":314295,"rank":"superfamily","names":{"Hominoidea":"scientific_name"},"parentid":9526,"name":"Hominoidea"}
{"taxid":9604,"rank":"family","names":{"Hominidae":"scientific_name"},"parentid":314295,"name":"Hominidae"}
{"taxid":207598,"rank":"subfamily","names":{"Homininae":"scientific_name"},"parentid":9604,"name":"Homininae"}
{"taxid":9605,"rank":"genus","names":{"Homo":"scientific_name"},"parentid":207598,"name":"Homo"}
{"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"na     me":"Homo sapiens"}
{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}
{"taxid":2,"rank":"superkingdom","names":{"Bacteria":"scientific_name","eubacteria":"GenbankCommonName","bacteria":"BlastName","Monera":"Inp     art","Procaryotae":"Inpart","Prokaryota":"Inpart","Prokaryotae":"Inpart","prokaryote":"Inpart","prokaryotes":"Inpart"},"parentid":131567,"na     me":"Bacteria"}
  • Check database:
sqlite3 taxa.db 'SELECT * FROM taxa t JOIN names n on t.taxonid=n.taxonid;'
id|taxonid|rank|parentid|id|taxonid|name|type
1|9606|species|9605|1|9606|Homo sapiens|scientific_name
1|9606|species|9605|2|9606|human|GenbankCommonName
1|9606|species|9605|3|9606|man|CommonName
2|9605|genus|207598|4|9605|Homo|scientific_name
3|207598|subfamily|9604|5|207598|Homininae|scientific_name
4|9604|family|314295|6|9604|Hominidae|scientific_name
5|314295|superfamily|9526|7|314295|Hominoidea|scientific_name
6|9526|parvorder|314293|8|9526|Catarrhini|scientific_name
7|314293|infraorder|376913|9|314293|Simiiformes|scientific_name
8|376913|suborder|9443|10|376913|Haplorrhini|scientific_name
9|9443|order|314146|11|9443|Primates|scientific_name
10|314146|superorder|1437010|12|314146|Euarchontoglires|scientific_name
11|1437010|clade|9347|13|1437010|Boreoeutheria|scientific_name
12|9347|clade|32525|14|9347|Eutheria|scientific_name
13|32525|clade|40674|15|32525|Theria|scientific_name
14|40674|class|32524|16|40674|Mammalia|scientific_name
15|32524|clade|32523|17|32524|Amniota|scientific_name
16|32523|clade|1338369|18|32523|Tetrapoda|scientific_name
17|1338369|clade|8287|19|1338369|Dipnotetrapodomorpha|scientific_name
18|8287|superclass|117571|20|8287|Sarcopterygii|scientific_name
19|117571|clade|117570|21|117571|Euteleostomi|scientific_name
20|117570|clade|7776|22|117570|Teleostomi|scientific_name
21|7776|clade|7742|23|7776|Gnathostomata|scientific_name
22|7742|clade|89593|24|7742|Vertebrata|scientific_name
23|89593|subphylum|7711|25|89593|Craniata|scientific_name
24|7711|phylum|33511|26|7711|Chordata|scientific_name
25|33511|clade|33213|27|33511|Deuterostomia|scientific_name
26|33213|clade|6072|28|33213|Bilateria|scientific_name
27|6072|clade|33208|29|6072|Eumetazoa|scientific_name
28|33208|kingdom|33154|30|33208|Metazoa|scientific_name
29|33154|clade|2759|31|33154|Opisthokonta|scientific_name
30|2759|superkingdom|131567|32|2759|Eukaryota|scientific_name
31|131567|no rank||33|131567|cellular organisms|scientific_name
32|2|superkingdom|131567|34|2|Bacteria|scientific_name
32|2|superkingdom|131567|35|2|eubacteria|GenbankCommonName
32|2|superkingdom|131567|36|2|bacteria|BlastName
32|2|superkingdom|131567|37|2|Monera|Inpart
32|2|superkingdom|131567|38|2|Procaryotae|Inpart
32|2|superkingdom|131567|39|2|Prokaryota|Inpart
32|2|superkingdom|131567|40|2|Prokaryotae|Inpart
32|2|superkingdom|131567|41|2|prokaryote|Inpart
32|2|superkingdom|131567|42|2|prokaryotes|Inpart

Import taxa via resolve

ncbi-taxonomist resolve  -n man -t 2 | ncbi-taxonomist import -db taxa-resolve.db
{"mode":"resolve","query":"man","cast":"taxon","taxon":{"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"},"lineage":[{"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"},{"taxid":9605,"rank":"genus","names":{"Homo":"scientific_name"},"parentid":207598,"name":"Homo"},{"taxid":207598,"rank":"subfamily","names":{"Homininae":"scientific_name"},"parentid":9604,"name":"Homininae"},{"taxid":9604,"rank":"family","names":{"Hominidae":"scientific_name"},"parentid":314295,"name":"Hominidae"},{"taxid":314295,"rank":"superfamily","names":{"Hominoidea":"scientific_name"},"parentid":9526,"name":"Hominoidea"},{"taxid":9526,"rank":"parvorder","names":{"Catarrhini":"scientific_name"},"parentid":314293,"name":"Catarrhini"},{"taxid":314293,"rank":"infraorder","names":{"Simiiformes":"scientific_name"},"parentid":376913,"name":"Simiiformes"},{"taxid":376913,"rank":"suborder","names":{"Haplorrhini":"scientific_name"},"parentid":9443,"name":"Haplorrhini"},{"taxid":9443,"rank":"order","names":{"Primates":"scientific_name"},"parentid":314146,"name":"Primates"},{"taxid":314146,"rank":"superorder","names":{"Euarchontoglires":"scientific_name"},"parentid":1437010,"name":"Euarchontoglires"},{"taxid":1437010,"rank":"clade","names":{"Boreoeutheria":"scientific_name"},"parentid":9347,"name":"Boreoeutheria"},{"taxid":9347,"rank":"clade","names":{"Eutheria":"scientific_name"},"parentid":32525,"name":"Eutheria"},{"taxid":32525,"rank":"clade","names":{"Theria":"scientific_name"},"parentid":40674,"name":"Theria"},{"taxid":40674,"rank":"class","names":{"Mammalia":"scientific_name"},"parentid":32524,"name":"Mammalia"},{"taxid":32524,"rank":"clade","names":{"Amniota":"scientific_name"},"parentid":32523,"name":"Amniota"},{"taxid":32523,"rank":"clade","names":{"Tetrapoda":"scientific_name"},"parentid":1338369,"name":"Tetrapoda"},{"taxid":1338369,"rank":"clade","names":{"Dipnotetrapodomorpha":"scientific_name"},"parentid":8287,"name":"Dipnotetrapodomorpha"},{"taxid":8287,"rank":"superclass","names":{"Sarcopterygii":"scientific_name"},"parentid":117571,"name":"Sarcopterygii"},{"taxid":117571,"rank":"clade","names":{"Euteleostomi":"scientific_name"},"parentid":117570,"name":"Euteleostomi"},{"taxid":117570,"rank":"clade","names":{"Teleostomi":"scientific_name"},"parentid":7776,"name":"Teleostomi"},{"taxid":7776,"rank":"clade","names":{"Gnathostomata":"scientific_name"},"parentid":7742,"name":"Gnathostomata"},{"taxid":7742,"rank":"clade","names":{"Vertebrata":"scientific_name"},"parentid":89593,"name":"Vertebrata"},{"taxid":89593,"rank":"subphylum","names":{"Craniata":"scientific_name"},"parentid":7711,"name":"Craniata"},{"taxid":7711,"rank":"phylum","names":{"Chordata":"scientific_name"},"parentid":33511,"name":"Chordata"},{"taxid":33511,"rank":"clade","names":{"Deuterostomia":"scientific_name"},"parentid":33213,"name":"Deuterostomia"},{"taxid":33213,"rank":"clade","names":{"Bilateria":"scientific_name"},"parentid":6072,"name":"Bilateria"},{"taxid":6072,"rank":"clade","names":{"Eumetazoa":"scientific_name"},"parentid":33208,"name":"Eumetazoa"},{"taxid":33208,"rank":"kingdom","names":{"Metazoa":"scientific_name"},"parentid":33154,"name":"Metazoa"},{"taxid":33154,"rank":"clade","names":{"Opisthokonta":"scientific_name"},"parentid":2759,"name":"Opisthokonta"},{"taxid":2759,"rank":"superkingdom","names":{"Eukaryota":"scientific_name"},"parentid":131567,"name":"Eukaryota"},{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}]}
{"mode":"resolve","query":"2","cast":"taxon","taxon":{"taxid":2,"rank":"superkingdom","names":{"Bacteria":"scientific_name","eubacteria":"GenbankCommonName","bacteria":"BlastName","Monera":"Inpart","Procaryotae":"Inpart","Prokaryota":"Inpart","Prokaryotae":"Inpart","prokaryote":"Inpart","prokaryotes":"Inpart"},"parentid":131567,"name":"Bacteria"},"lineage":[{"taxid":2,"rank":"superkingdom","names":{"Bacteria":"scientific_name","eubacteria":"GenbankCommonName","bacteria":"BlastName","Monera":"Inpart","Procaryotae":"Inpart","Prokaryota":"Inpart","Prokaryotae":"Inpart","prokaryote":"Inpart","prokaryotes":"Inpart"},"parentid":131567,"name":"Bacteria"},{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}]}
  • Check database: The database should be identical to the database created with the collect command above.
sqlite3 taxa-resolve.db 'SELECT * FROM taxa t JOIN names n ON t.taxonid=n.taxonid;'

Import accessions

Importing accessions does not inmport only the taxid for the accession, not any other taxon metadata.
ncbi-taxonomist map --entrezdb protein --accessions  AFR11853 AIA66128.1 | ncbi-taxonomist import -db taxa.db
  • Check database:
sqlite3 -header taxa.db 'SELECT * FROM accessions a JOIN taxa t ON a.taxonid==t.taxonid;'
id|accession|db|type|uid|taxonid|id|taxonid|rank|parentid
1|AIA66128.1|protein|accessionversion|641483259|1239567|33|1239567||
2|AIA66128|protein|caption|641483259|1239567|33|1239567||
3|gi|641483259|gb|AIA66128.1||protein|extra|641483259|1239567|33|1239567||
4|AFR11853.1|protein|accessionversion|403044789|1224525|34|1224525||
5|AFR11853|protein|caption|403044789|1224525|34|1224525||
6|gi|403044789|gb|AFR11853.1||protein|extra|403044789|1224525|34|1224525||

To add the missing information, please check Importing accessions for an extended command accomplishing this. The following example shows the database after adding the missing data:

sqlite3 -header taxa.db 'SELECT * FROM accessions a JOIN taxa t ON a.taxonid==t.taxonid;'
id|accession|db|type|uid|taxonid|id|taxonid|rank|parentid
1|AIA66128.1|protein|accessionversion|641483259|1239567|33|1239567|species|249588
2|AIA66128|protein|caption|641483259|1239567|33|1239567|species|249588
3|gi|641483259|gb|AIA66128.1||protein|extra|641483259|1239567|33|1239567|species|249588
4|AFR11853.1|protein|accessionversion|403044789|1224525|34|1224525|species|35278
5|AFR11853|protein|caption|403044789|1224525|34|1224525|species|35278
6|gi|403044789|gb|AFR11853.1||protein|extra|403044789|1224525|34|1224525|species|35278

Subtree

ncbi-taxonomist subtree collects taxonomic subsamples for taxids or names in a local database.

Note

Fetching subtrees remotely form Entrez is in development.

A local database is required, for example:

$: ncbi-taxonomist collect -t 142786 9606 | ncbi-taxonomist import -db test.db

Collecting subtrees

Between two given ranks

$: ncbi-taxonomist subtree -db test.db -t 142786 9606 --lrank order --hrank phylum
{"mode":"subtree","query":9606,"subtree":[{"taxid":9443,"rank":"order","names":{"Primates":"scientific_name"},"parentid":314146,"name":"Primates"},{"taxid":314146,"rank":"superorder","names":{"Euarchontoglires":"scientific_name"},"parentid":1437010,"name":"Euarchontoglires"},{"taxid":1437010,"rank":"clade","names":{"Boreoeutheria":"scientific_name"},"parentid":9347,"name":"Boreoeutheria"},{"taxid":9347,"rank":"clade","names":{"Eutheria":"scientific_name"},"parentid":32525,"name":"Eutheria"},{"taxid":32525,"rank":"clade","names":{"Theria":"scientific_name"},"parentid":40674,"name":"Theria"},{"taxid":40674,"rank":"class","names":{"Mammalia":"scientific_name"},"parentid":32524,"name":"Mammalia"},{"taxid":32524,"rank":"clade","names":{"Amniota":"scientific_name"},"parentid":32523,"name":"Amniota"},{"taxid":32523,"rank":"clade","names":{"Tetrapoda":"scientific_name"},"parentid":1338369,"name":"Tetrapoda"},{"taxid":1338369,"rank":"clade","names":{"Dipnotetrapodomorpha":"scientific_name"},"parentid":8287,"name":"Dipnotetrapodomorpha"},{"taxid":8287,"rank":"superclass","names":{"Sarcopterygii":"scientific_name"},"parentid":117571,"name":"Sarcopterygii"},{"taxid":117571,"rank":"clade","names":{"Euteleostomi":"scientific_name"},"parentid":117570,"name":"Euteleostomi"},{"taxid":117570,"rank":"clade","names":{"Teleostomi":"scientific_name"},"parentid":7776,"name":"Teleostomi"},{"taxid":7776,"rank":"clade","names":{"Gnathostomata":"scientific_name"},"parentid":7742,"name":"Gnathostomata"},{"taxid":7742,"rank":"clade","names":{"Vertebrata":"scientific_name"},"parentid":89593,"name":"Vertebrata"},{"taxid":89593,"rank":"subphylum","names":{"Craniata":"scientific_name"},"parentid":7711,"name":"Craniata"},{"taxid":7711,"rank":"phylum","names":{"Chordata":"scientific_name"},"parentid":33511,"name":"Chordata"}]}
{"mode":"subtree","query":142786,"subtree":[{"taxid":464095,"rank":"order","names":{"Picornavirales":"scientific_name"},"parentid":2732506,"name":"Picornavirales"},{"taxid":2732506,"rank":"class","names":{"Pisoniviricetes":"scientific_name"},"parentid":2732408,"name":"Pisoniviricetes"},{"taxid":2732408,"rank":"phylum","names":{"Pisuviricota":"scientific_name"},"parentid":2732396,"name":"Pisuviricota"}]}

Collect one specific rank

$: ncbi-taxonomist subtree -db test.db -t 142786 9606 --rank order
{"mode":"subtree","query":9606,"subtree":[{"taxid":9443,"rank":"order","names":{"Primates":"scientific_name"},"parentid":314146,"name":"Primates"}]}
{"mode":"subtree","query":142786,"subtree":[{"taxid":464095,"rank":"order","names":{"Picornavirales":"scientific_name"},"parentid":2732506,"name":"Picornavirales"}]

Collect from a given rank to root and print XML

$: ncbi-taxonomist subtree -x -db test.db -t 142786 9606 --lrank order
<subtree><query value="9606" cast="taxid" /><tree><taxon><taxid>9443</taxid><rank>order</rank><name>Primates</name><parentid>314146</parentid><names><name type="scientific_name">Primates</name></names></taxon><taxon><taxid>314146</taxid><rank>superorder</rank><name>Euarchontoglires</name><parentid>1437010</parentid><names><name type="scientific_name">Euarchontoglires</name></names></taxon><taxon><taxid>1437010</taxid><rank>clade</rank><name>Boreoeutheria</name><parentid>9347</parentid><names><name type="scientific_name">Boreoeutheria</name></names></taxon><taxon><taxid>9347</taxid><rank>clade</rank><name>Eutheria</name><parentid>32525</parentid><names><name type="scientific_name">Eutheria</name></names></taxon><taxon><taxid>32525</taxid><rank>clade</rank><name>Theria</name><parentid>40674</parentid><names><name type="scientific_name">Theria</name></names></taxon><taxon><taxid>40674</taxid><rank>class</rank><name>Mammalia</name><parentid>32524</parentid><names><name type="scientific_name">Mammalia</name></names></taxon><taxon><taxid>32524</taxid><rank>clade</rank><name>Amniota</name><parentid>32523</parentid><names><name type="scientific_name">Amniota</name></names></taxon><taxon><taxid>32523</taxid><rank>clade</rank><name>Tetrapoda</name><parentid>1338369</parentid><names><name type="scientific_name">Tetrapoda</name></names></taxon><taxon><taxid>1338369</taxid><rank>clade</rank><name>Dipnotetrapodomorpha</name><parentid>8287</parentid><names><name type="scientific_name">Dipnotetrapodomorpha</name></names></taxon><taxon><taxid>8287</taxid><rank>superclass</rank><name>Sarcopterygii</name><parentid>117571</parentid><names><name type="scientific_name">Sarcopterygii</name></names></taxon><taxon><taxid>117571</taxid><rank>clade</rank><name>Euteleostomi</name><parentid>117570</parentid><names><name type="scientific_name">Euteleostomi</name></names></taxon><taxon><taxid>117570</taxid><rank>clade</rank><name>Teleostomi</name><parentid>7776</parentid><names><name type="scientific_name">Teleostomi</name></names></taxon><taxon><taxid>7776</taxid><rank>clade</rank><name>Gnathostomata</name><parentid>7742</parentid><names><name type="scientific_name">Gnathostomata</name></names></taxon><taxon><taxid>7742</taxid><rank>clade</rank><name>Vertebrata</name><parentid>89593</parentid><names><name type="scientific_name">Vertebrata</name></names></taxon><taxon><taxid>89593</taxid><rank>subphylum</rank><name>Craniata</name><parentid>7711</parentid><names><name type="scientific_name">Craniata</name></names></taxon><taxon><taxid>7711</taxid><rank>phylum</rank><name>Chordata</name><parentid>33511</parentid><names><name type="scientific_name">Chordata</name></names></taxon><taxon><taxid>33511</taxid><rank>clade</rank><name>Deuterostomia</name><parentid>33213</parentid><names><name type="scientific_name">Deuterostomia</name></names></taxon><taxon><taxid>33213</taxid><rank>clade</rank><name>Bilateria</name><parentid>6072</parentid><names><name type="scientific_name">Bilateria</name></names></taxon><taxon><taxid>6072</taxid><rank>clade</rank><name>Eumetazoa</name><parentid>33208</parentid><names><name type="scientific_name">Eumetazoa</name></names></taxon><taxon><taxid>33208</taxid><rank>kingdom</rank><name>Metazoa</name><parentid>33154</parentid><names><name type="scientific_name">Metazoa</name></names></taxon><taxon><taxid>33154</taxid><rank>clade</rank><name>Opisthokonta</name><parentid>2759</parentid><names><name type="scientific_name">Opisthokonta</name></names></taxon><taxon><taxid>2759</taxid><rank>superkingdom</rank><name>Eukaryota</name><parentid>131567</parentid><names><name type="scientific_name">Eukaryota</name></names></taxon><taxon><taxid>131567</taxid><rank>no rank</rank><name>cellular organisms</name><parentid>None</parentid><names><name type="scientific_name">cellular organisms</name></names></taxon></tree></subtree>
<subtree><query value="142786" cast="taxid" /><tree><taxon><taxid>464095</taxid><rank>order</rank><name>Picornavirales</name><parentid>2732506</parentid><names><name type="scientific_name">Picornavirales</name></names></taxon><taxon><taxid>2732506</taxid><rank>class</rank><name>Pisoniviricetes</name><parentid>2732408</parentid><names><name type="scientific_name">Pisoniviricetes</name></names></taxon><taxon><taxid>2732408</taxid><rank>phylum</rank><name>Pisuviricota</name><parentid>2732396</parentid><names><name type="scientific_name">Pisuviricota</name></names></taxon><taxon><taxid>2732396</taxid><rank>kingdom</rank><name>Orthornavirae</name><parentid>2559587</parentid><names><name type="scientific_name">Orthornavirae</name></names></taxon><taxon><taxid>2559587</taxid><rank>clade</rank><name>Riboviria</name><parentid>10239</parentid><names><name type="scientific_name">Riboviria</name></names></taxon><taxon><taxid>10239</taxid><rank>superkingdom</rank><name>Viruses</name><parentid>None</parentid><names><name type="scientific_name">Viruses</name></names></taxon></tree></subtree>

Collect from a given rank to lowest rank

$: ncbi-taxonomist subtree  -db test.db -t 142786 9606 --hrank order
{"mode":"subtree","query":9606,"subtree":[{"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"},{"taxid":9605,"rank":"genus","names":{"Homo":"scientific_name"},"parentid":207598,"name":"Homo"},{"taxid":207598,"rank":"subfamily","names":{"Homininae":"scientific_name"},"parentid":9604,"name":"Homininae"},{"taxid":9604,"rank":"family","names":{"Hominidae":"scientific_name"},"parentid":314295,"name":"Hominidae"},{"taxid":314295,"rank":"superfamily","names":{"Hominoidea":"scientific_name"},"parentid":9526,"name":"Hominoidea"},{"taxid":9526,"rank":"parvorder","names":{"Catarrhini":"scientific_name"},"parentid":314293,"name":"Catarrhini"},{"taxid":314293,"rank":"infraorder","names":{"Simiiformes":"scientific_name"},"parentid":376913,"name":"Simiiformes"},{"taxid":376913,"rank":"suborder","names":{"Haplorrhini":"scientific_name"},"parentid":9443,"name":"Haplorrhini"},{"taxid":9443,"rank":"order","names":{"Primates":"scientific_name"},"parentid":314146,"name":"Primates"}]}
{"mode":"subtree","query":142786,"subtree":[{"taxid":142786,"rank":"genus","names":{"Norovirus":"scientific_name","Norwalk-like viruses":"EquivalentName"},"parentid":11974,"name":"Norovirus"},{"taxid":11974,"rank":"family","names":{"Caliciviridae":"scientific_name"},"parentid":464095,"name":"Caliciviridae"},{"taxid":464095,"rank":"order","names":{"Picornavirales":"scientific_name"},"parentid":2732506,"name":"Picornavirales"}]}

Output format

JSON output

{
  "mode": "subtree",
  "query": 9606,
  "subtree": [
    {
      "taxid": 9443,
      "rank": "order",
      "names": {
        "Primates": "scientific_name"
      },
      "parentid": 314146,
      "name": "Primates"
    },
    {
      "taxid": 314146,
      "rank": "superorder",
      "names": {
        "Euarchontoglires": "scientific_name"
      },
      "parentid": 1437010,
      "name": "Euarchontoglires"
    },
    {
      "taxid": 1437010,
      "rank": "clade",
      "names": {
        "Boreoeutheria": "scientific_name"
      },
      "parentid": 9347,
      "name": "Boreoeutheria"
    },
    {
      "taxid": 9347,
      "rank": "clade",
      "names": {
        "Eutheria": "scientific_name"
      },
      "parentid": 32525,
      "name": "Eutheria"
    },
    {
      "taxid": 32525,
      "rank": "clade",
      "names": {
        "Theria": "scientific_name"
      },
      "parentid": 40674,
      "name": "Theria"
    },
    {
      "taxid": 40674,
      "rank": "class",
      "names": {
        "Mammalia": "scientific_name"
      },
      "parentid": 32524,
      "name": "Mammalia"
    },
    {
      "taxid": 32524,
      "rank": "clade",
      "names": {
        "Amniota": "scientific_name"
      },
      "parentid": 32523,
      "name": "Amniota"
    },
    {
      "taxid": 32523,
      "rank": "clade",
      "names": {
        "Tetrapoda": "scientific_name"
      },
      "parentid": 1338369,
      "name": "Tetrapoda"
    },
    {
      "taxid": 1338369,
      "rank": "clade",
      "names": {
        "Dipnotetrapodomorpha": "scientific_name"
      },
      "parentid": 8287,
      "name": "Dipnotetrapodomorpha"
    },
    {
      "taxid": 8287,
      "rank": "superclass",
      "names": {
        "Sarcopterygii": "scientific_name"
      },
      "parentid": 117571,
      "name": "Sarcopterygii"
    },
    {
      "taxid": 117571,
      "rank": "clade",
      "names": {
        "Euteleostomi": "scientific_name"
      },
      "parentid": 117570,
      "name": "Euteleostomi"
    },
    {
      "taxid": 117570,
      "rank": "clade",
      "names": {
        "Teleostomi": "scientific_name"
      },
      "parentid": 7776,
      "name": "Teleostomi"
    },
    {
      "taxid": 7776,
      "rank": "clade",
      "names": {
        "Gnathostomata": "scientific_name"
      },
      "parentid": 7742,
      "name": "Gnathostomata"
    },
    {
      "taxid": 7742,
      "rank": "clade",
      "names": {
        "Vertebrata": "scientific_name"
      },
      "parentid": 89593,
      "name": "Vertebrata"
    },
    {
      "taxid": 89593,
      "rank": "subphylum",
      "names": {
        "Craniata": "scientific_name"
      },
      "parentid": 7711,
      "name": "Craniata"
    },
    {
      "taxid": 7711,
      "rank": "phylum",
      "names": {
        "Chordata": "scientific_name"
      },
      "parentid": 33511,
      "name": "Chordata"
    }
  ]
}
{
  "mode": "subtree",
  "query": 142786,
  "subtree": [
    {
      "taxid": 464095,
      "rank": "order",
      "names": {
        "Picornavirales": "scientific_name"
      },
      "parentid": 2732506,
      "name": "Picornavirales"
    },
    {
      "taxid": 2732506,
      "rank": "class",
      "names": {
        "Pisoniviricetes": "scientific_name"
      },
      "parentid": 2732408,
      "name": "Pisoniviricetes"
    },
    {
      "taxid": 2732408,
      "rank": "phylum",
      "names": {
        "Pisuviricota": "scientific_name"
      },
      "parentid": 2732396,
      "name": "Pisuviricota"
    }
  ]
}

XML output

<subtree>
<query value="9606" cast="taxid" />
<tree>
  <taxon>
    <taxid>9443</taxid>
    <rank>order</rank>
    <name>Primates</name>
    <parentid>314146</parentid>
    <names>
      <name type="scientific_name">Primates</name>
    </names>
  </taxon>
  <taxon>
    <taxid>314146</taxid>
    <rank>superorder</rank>
    <name>Euarchontoglires</name>
    <parentid>1437010</parentid>
    <names>
      <name type="scientific_name">Euarchontoglires</name>
    </names>
  </taxon>
  <taxon>
    <taxid>1437010</taxid>
    <rank>clade</rank>
    <name>Boreoeutheria</name>
    <parentid>9347</parentid>
    <names>
      <name type="scientific_name">Boreoeutheria</name>
    </names>
  </taxon>
  <taxon>
    <taxid>9347</taxid>
    <rank>clade</rank>
    <name>Eutheria</name>
    <parentid>32525</parentid>
    <names>
      <name type="scientific_name">Eutheria</name>
    </names>
  </taxon>
  <taxon>
    <taxid>32525</taxid>
    <rank>clade</rank>
    <name>Theria</name>
    <parentid>40674</parentid>
    <names>
      <name type="scientific_name">Theria</name>
    </names>
  </taxon>
  <taxon>
    <taxid>40674</taxid>
    <rank>class</rank>
    <name>Mammalia</name>
    <parentid>32524</parentid>
    <names>
      <name type="scientific_name">Mammalia</name>
    </names>
  </taxon>
  <taxon>
    <taxid>32524</taxid>
    <rank>clade</rank>
    <name>Amniota</name>
    <parentid>32523</parentid>
    <names>
      <name type="scientific_name">Amniota</name>
    </names>
  </taxon>
  <taxon>
    <taxid>32523</taxid>
    <rank>clade</rank>
    <name>Tetrapoda</name>
    <parentid>1338369</parentid>
    <names>
      <name type="scientific_name">Tetrapoda</name>
    </names>
  </taxon>
  <taxon>
    <taxid>1338369</taxid>
    <rank>clade</rank>
    <name>Dipnotetrapodomorpha</name>
    <parentid>8287</parentid>
    <names>
      <name type="scientific_name">Dipnotetrapodomorpha</name>
    </names>
  </taxon>
  <taxon>
    <taxid>8287</taxid>
    <rank>superclass</rank>
    <name>Sarcopterygii</name>
    <parentid>117571</parentid>
    <names>
      <name type="scientific_name">Sarcopterygii</name>
    </names>
  </taxon>
  <taxon>
    <taxid>117571</taxid>
    <rank>clade</rank>
    <name>Euteleostomi</name>
    <parentid>117570</parentid>
    <names>
      <name type="scientific_name">Euteleostomi</name>
    </names>
  </taxon>
  <taxon>
    <taxid>117570</taxid>
    <rank>clade</rank>
    <name>Teleostomi</name>
    <parentid>7776</parentid>
    <names>
      <name type="scientific_name">Teleostomi</name>
    </names>
  </taxon>
  <taxon>
    <taxid>7776</taxid>
    <rank>clade</rank>
    <name>Gnathostomata</name>
    <parentid>7742</parentid>
    <names>
      <name type="scientific_name">Gnathostomata</name>
    </names>
  </taxon>
  <taxon>
    <taxid>7742</taxid>
    <rank>clade</rank>
    <name>Vertebrata</name>
    <parentid>89593</parentid>
    <names>
      <name type="scientific_name">Vertebrata</name>
    </names>
  </taxon>
  <taxon>
    <taxid>89593</taxid>
    <rank>subphylum</rank>
    <name>Craniata</name>
    <parentid>7711</parentid>
    <names>
      <name type="scientific_name">Craniata</name>
    </names>
  </taxon>
  <taxon>
    <taxid>7711</taxid>
    <rank>phylum</rank>
    <name>Chordata</name>
    <parentid>33511</parentid>
    <names>
      <name type="scientific_name">Chordata</name>
    </names>
  </taxon>
</tree>
</subtree>

Group

ncbi-taxonomist group creates and lists taxonomix groups in a local ncbi-taxonomist database.

Creating a group

$: ncbi-taxonomist collect -n 'Black willow' 'Black hickory' | \
   ncbi-taxonomist import -db taxa.db                        | \
  ncbi-taxonomist group --add tree -db taxa.db

Retrieve a group

Groups can be retrieved as taxids and processed, e.g. with jq, and reused.

$: ncbi-taxonomist group --get tree -db taxa.db  | \
   jq '.taxa[]'                                  | \
  ncbi-taxonomist map -t -db taxa.db