Metadata-Version: 2.1
Name: ncbi-taxonomist
Version: 1.2.1
Summary: Toolbox to manage NCBI taxonomical data
Home-page: https://gitlab.com/janpb/ncbi-taxonomist.git
Author: Jan P Buchmann
Author-email: jpb@members.fsf.org
License: LGPL
Project-URL: Doc, https://ncbi-taxonomist.readthedocs.io/
Project-URL: Code, https://gitlab.com/janpb/ncbi-taxonomist.git
Keywords: bioinformatics NCBI taxonomy
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.8
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: entrezpy (>=2.1.0)

# Readme

## Synopsis

ncbi-taxonomist handles and manages phylogenetic data from NCBI's Entrez
[taxonomy database](https://www.ncbi.nlm.nih.gov/taxonomy) . It can:

  - fetch information from Entrez' Taxonomy database
  - map between taxids and names
  - resolve lineages for taxid, names, and accessions
  - store obtained taxa and their data locally in a SQLite database
  - group taxa into user defined groups (locally)
  - extract specific ranks or lineages from subtrees

`ncbi-taxonomist` has several simple operations, e.g. `map` or `import`, which
work together using pipes, e.g. to populate a database, `collect` will fetch
data from Entrez and print it to STDOUT while `import` reads the STDIN to
populate a local database. Taxonomic information is obtained from Entrez.

## Install

```$pip install ncbi-taxonomist --user```

This will fetch and install `ncbi-taxonomist` and its required dependencies
(see below) use for an user (no `root` required).

### Containers

`ncbi-taxonomist` is available as Docker and Singularity image including
[`jq`](https://stedolan.github.io/jq/) to manipulate its JSON output.

#### Docker

The Docker image is available on its
[GitLab Docker registry](https://gitlab.com/janpb/ncbi-taxonomist/container_registry)
and can be pulled using `docker pull registry.gitlab.com/janpb/ncbi-taxonomist/ncbi-taxonomist:latest`.

#### Singularity

The Singularity image is available in the
[Singularity library](https://cloud.sylabs.io/library/jpb/ncbi-taxonomist)
and can be pulled using `singularity pull library://jpb/ncbi-taxonomist/ncbi-taxonomist`.


### Dependencies

`ncbi-taxonomist` has one dependency:

  - `entrezpy`: to handle remote requests to NCBI's Entrez databases

    - [Source](https://gitlab.com/ncbipy/entrezpy.git)
    - [PyPi](https://pypi.org/project/entrezpy/)
    - [Publication](https://doi.org/10.1093/bioinformatics/btz385)

`entrezpy` is developed and maintained by myself and a collaboration with Prof.
Edward C. Holmes at The University of Sydney. It relies  solely on the Python
standard library. Therefore, `ncbi-taxonomist` is less prone to suffer
[dependency hell](https://en.wikipedia.org/wiki/Dependency_hell).

## Documentation

The documentation and further examples for `ncbi-taxonomist` can be found
on [`Read the Docs`](https://ncbi-taxonomist.readthedocs.io/en/latest/).

## Usage

**`ncbi-taxonomist <command> <options>`**

### Available commands

call without any command or option  to  get an overview of available commands.

**`$ ncbi-taxonomist`**

### Command help

To get the usage for a specific command, use:

**`$ ncbi-taxonomist <command> -h`**

For example, to see available options for the command `map`, use:

**`$ ncbi-taxonomist map -h`**

## Output

`ncbi-taxonist` uses line based `JSON` and `XML` as output because I have no clue what
you want to do with the result. Parsing `JSON` is simpler than `XML` (IMHO) and
most programming languages have a `JSON` parser in their standard library. This
allows to write quick formatter or viewers reading data directly from `STDIN`.

`XML` output os provided for convenience, but cannot be used between piped
`ncbi-taxonomist` commands, only in the last command.

In addition, [`jq`](https://stedolan.github.io/jq/) is an excellent tool to
filter and manipulate `JSON` data. An example how to extract attributes from the
`ncbi-taxonomist map` command `JSON` output can be found in the
[documentation](https://ncbi-taxonomist.readthedocs.io/en/latest/cookbook.html):

For more `jq` help, please refer to:

  - [`jq` manual](https://stedolan.github.io/jq/manual/)
  - [Matthew Lincoln, "Reshaping JSON with jq," The Programming Historian 5 (2016)](https://programminghistorian.org/en/lessons/json-and-jq)


## Basic Commands

Examples how to use the basic commands. To get an overview, run ncbi-taxonomist
without any argument:

```
$: ncbi-taxonomist
```

Use `-h` to get the usage for each command, e.g.:

```
$: ncbi-taxonomist map -h
```

### `map`

map taxonomic information from Entrez phylogeny server or loading a downloaded
NCBI Taxonomy database into a local database. Returns taxonomic nodes in `JSON`.

#### Map taxid and names

```
$: ncbi-taxonomist map --taxids 562, 10508 --names 'Homo sapiens', 'black willow'
{"mode":"mapping","query":"black willow","cast":"taxon","taxon":{"taxid":75714,"rank":"species","names":{"Salix nigra":"scientific_name","black willow":"CommonName"},"parentid":40685,"name":"Salix nigra"}}
{"mode":"mapping","query":"Homo sapiens","cast":"taxon","taxon":{"taxid":9606,"rank":"species","names":{"Homo sapiens":"scientific_name","human":"GenbankCommonName","man":"CommonName"},"parentid":9605,"name":"Homo sapiens"}}
{"mode":"mapping","query":"10508","cast":"taxon","taxon":{"taxid":10508,"rank":"family","names":{"Adenoviridae":"scientific_name"},"parentid":2732559,"name":"Adenoviridae"}}
{"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"}}

ncbi-taxonomist map --xml --taxids 562
<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>
```

#### Map accessions

```
$: ncbi-taxonomist map --accessions MH842226.1 NQWZ01000003 --entrezdb nucleotide
{"mode":"mapping","query":"NQWZ01000003","cast":"accs","accession":{"taxid":45151,"accessions":{"accessionversion":"NQWZ01000003.1","caption":"NQWZ01000003","extra":"gi|1391950314|gb|NQWZ01000003.1||gnl|WGS:NQWZ01|ARCrossB10_scaffold_00003"},"db":"nucleotide","uid":1391950314}}
{"mode":"mapping","query":"MH842226.1","cast":"accs","accession":{"taxid":122929,"accessions":{"accessionversion":"MH842226.1","caption":"MH842226","extra":"gi|1476663987|gb|MH842226.1|"},"db":"nucleotide","uid":1476663987}}

$: ncbi-taxonomist map --xml --accessions AGA95798 --entrezdb protein
<mapping><query cast="accession">AGA95798</query><accession><taxid>10407</taxid><uid>431983379</uid><database>protein</database><accessions><accessionversion>AGA95798.1</accessionversion><caption>AGA95798</caption><extra>gi|431983379|gb|AGA95798.1|</extra></accessions></accession></mapping>
```
### Resolve lineages for names, taxids, and accessions.

#### Resolve names and taxids remotely:

```
$: ncbi-taxonomist resolve -t 562, 10508 -n human, 'black willow'
{"mode":"resolve","query":"black willow","cast":"taxon","taxon":{"taxid":75714,"rank":"species","names":{"Salix nigra":"scientific_name","black willow":"CommonName"},"parentid":40685,"name":"Salix nigra"},"lineage":[{"taxid":75714,"rank":"species","names":{"Salix nigra":"scientific_name","black willow":"CommonName"},"parentid":40685,"name":"Salix nigra"},{"taxid":40685,"rank":"genus","names":{"Salix":"scientific_name"},"parentid":238069,"name":"Salix"},{"taxid":238069,"rank":"tribe","names":{"Saliceae":"scientific_name"},"parentid":3688,"name":"Saliceae"},{"taxid":3688,"rank":"family","names":{"Salicaceae":"scientific_name"},"parentid":3646,"name":"Salicaceae"},{"taxid":3646,"rank":"order","names":{"Malpighiales":"scientific_name"},"parentid":91835,"name":"Malpighiales"},{"taxid":91835,"rank":"clade","names":{"fabids":"scientific_name"},"parentid":71275,"name":"fabids"},{"taxid":71275,"rank":"clade","names":{"rosids":"scientific_name"},"parentid":1437201,"name":"rosids"},{"taxid":1437201,"rank":"clade","names":{"Pentapetalae":"scientific_name"},"parentid":91827,"name":"Pentapetalae"},{"taxid":91827,"rank":"clade","names":{"Gunneridae":"scientific_name"},"parentid":71240,"name":"Gunneridae"},{"taxid":71240,"rank":"clade","names":{"eudicotyledons":"scientific_name"},"parentid":1437183,"name":"eudicotyledons"},{"taxid":1437183,"rank":"clade","names":{"Mesangiospermae":"scientific_name"},"parentid":3398,"name":"Mesangiospermae"},{"taxid":3398,"rank":"class","names":{"Magnoliopsida":"scientific_name"},"parentid":58024,"name":"Magnoliopsida"},{"taxid":58024,"rank":"clade","names":{"Spermatophyta":"scientific_name"},"parentid":78536,"name":"Spermatophyta"},{"taxid":78536,"rank":"clade","names":{"Euphyllophyta":"scientific_name"},"parentid":58023,"name":"Euphyllophyta"},{"taxid":58023,"rank":"clade","names":{"Tracheophyta":"scientific_name"},"parentid":3193,"name":"Tracheophyta"},{"taxid":3193,"rank":"clade","names":{"Embryophyta":"scientific_name"},"parentid":131221,"name":"Embryophyta"},{"taxid":131221,"rank":"subphylum","names":{"Streptophytina":"scientific_name"},"parentid":35493,"name":"Streptophytina"},{"taxid":35493,"rank":"phylum","names":{"Streptophyta":"scientific_name"},"parentid":33090,"name":"Streptophyta"},{"taxid":33090,"rank":"kingdom","names":{"Viridiplantae":"scientific_name"},"parentid":2759,"name":"Viridiplantae"},{"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":"human","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":"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"},"lineage":[{"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"},{"taxid":561,"rank":"genus","names":{"Escherichia":"scientific_name"},"parentid":543,"name":"Escherichia"},{"taxid":543,"rank":"family","names":{"Enterobacteriaceae":"scientific_name"},"parentid":91347,"name":"Enterobacteriaceae"},{"taxid":91347,"rank":"order","names":{"Enterobacterales":"scientific_name"},"parentid":1236,"name":"Enterobacterales"},{"taxid":1236,"rank":"class","names":{"Gammaproteobacteria":"scientific_name"},"parentid":1224,"name":"Gammaproteobacteria"},{"taxid":1224,"rank":"phylum","names":{"Proteobacteria":"scientific_name"},"parentid":2,"name":"Proteobacteria"},{"taxid":2,"rank":"superkingdom","names":{"Bacteria":"scientific_name"},"parentid":131567,"name":"Bacteria"},{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}]}
{"mode":"resolve","query":"10508","cast":"taxon","taxon":{"taxid":10508,"rank":"family","names":{"Adenoviridae":"scientific_name"},"parentid":2732559,"name":"Adenoviridae"},"lineage":[{"taxid":10508,"rank":"family","names":{"Adenoviridae":"scientific_name"},"parentid":2732559,"name":"Adenoviridae"},{"taxid":2732559,"rank":"order","names":{"Rowavirales":"scientific_name"},"parentid":2732529,"name":"Rowavirales"},{"taxid":2732529,"rank":"class","names":{"Tectiliviricetes":"scientific_name"},"parentid":2732008,"name":"Tectiliviricetes"},{"taxid":2732008,"rank":"phylum","names":{"Preplasmiviricota":"scientific_name"},"parentid":2732005,"name":"Preplasmiviricota"},{"taxid":2732005,"rank":"kingdom","names":{"Bamfordvirae":"scientific_name"},"parentid":2732004,"name":"Bamfordvirae"},{"taxid":2732004,"rank":"clade","names":{"Varidnaviria":"scientific_name"},"parentid":10239,"name":"Varidnaviria"},{"taxid":10239,"rank":"superkingdom","names":{"Viruses":"scientific_name"},"parentid":null,"name":"Viruses"}]}

$: ncbi-taxonomist resolve -x -t 562
<resolve><query value="562" cast="taxid"><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></query><lineage><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><taxon><taxid>561</taxid><rank>genus</rank><name>Escherichia</name><parentid>543</parentid><names><name type="scientific_name">Escherichia</name></names></taxon><taxon><taxid>543</taxid><rank>family</rank><name>Enterobacteriaceae</name><parentid>91347</parentid><names><name type="scientific_name">Enterobacteriaceae</name></names></taxon><taxon><taxid>91347</taxid><rank>order</rank><name>Enterobacterales</name><parentid>1236</parentid><names><name type="scientific_name">Enterobacterales</name></names></taxon><taxon><taxid>1236</taxid><rank>class</rank><name>Gammaproteobacteria</name><parentid>1224</parentid><names><name type="scientific_name">Gammaproteobacteria</name></names></taxon><taxon><taxid>1224</taxid><rank>phylum</rank><name>Proteobacteria</name><parentid>2</parentid><names><name type="scientific_name">Proteobacteria</name></names></taxon><taxon><taxid>2</taxid><rank>superkingdom</rank><name>Bacteria</name><parentid>131567</parentid><names><name type="scientific_name">Bacteria</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 accessions

Accessions have to be mapped prior to resolve.

```
$: ncbi-taxonomist map  -a MH842226.1 NQWZ01000003.1 | ncbi-taxonomist resolve --mapping
{"mode":"resolve","query":"MH842226.1","cast":"accs","accs":{"taxid":122929,"accessions":{"accessionversion":"MH842226.1","caption":"MH842226","extra":"gi|1476663987|gb|MH842226.1|"},"db":"nucleotide","uid":1476663987},"lineage":[{"taxid":122929,"rank":"clade","names":{"Norovirus GII":"scientific_name","Norovirus genogroup 2":"EquivalentName","Norovirus genogroup II":"EquivalentName","Norwalk-like virus genogroup 2":"EquivalentName","Norwalk-like viruses genogroup 2":"EquivalentName","human calicivirus genogroup 2":"EquivalentName"},"parentid":11983,"name":"Norovirus GII"},{"taxid":11983,"rank":"species","names":{"Norwalk virus":"scientific_name"},"parentid":142786,"name":"Norwalk virus"},{"taxid":142786,"rank":"genus","names":{"Norovirus":"scientific_name"},"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"},{"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"}]}
{"mode":"resolve","query":"NQWZ01000003.1","cast":"accs","accs":{"taxid":45151,"accessions":{"accessionversion":"NQWZ01000003.1","caption":"NQWZ01000003","extra":"gi|1391950314|gb|NQWZ01000003.1||gnl|WGS:NQWZ01|ARCrossB10_scaffold_00003"},"db":"nucleotide","uid":1391950314},"lineage":[{"taxid":45151,"rank":"species","names":{"Pyrenophora tritici-repentis":"scientific_name","Drechslera tritici-repentis":"Synonym","Pyrenophora triticirepentis":"Synonym","Pyrenophora sp. CBS 259.59":"Includes","Pyrenophora sp. MUCL 18687":"Includes"},"parentid":5027,"name":"Pyrenophora tritici-repentis"},{"taxid":5027,"rank":"genus","names":{"Pyrenophora":"scientific_name"},"parentid":28556,"name":"Pyrenophora"},{"taxid":28556,"rank":"family","names":{"Pleosporaceae":"scientific_name"},"parentid":715340,"name":"Pleosporaceae"},{"taxid":715340,"rank":"suborder","names":{"Pleosporineae":"scientific_name"},"parentid":92860,"name":"Pleosporineae"},{"taxid":92860,"rank":"order","names":{"Pleosporales":"scientific_name"},"parentid":451868,"name":"Pleosporales"},{"taxid":451868,"rank":"subclass","names":{"Pleosporomycetidae":"scientific_name"},"parentid":147541,"name":"Pleosporomycetidae"},{"taxid":147541,"rank":"class","names":{"Dothideomycetes":"scientific_name"},"parentid":715962,"name":"Dothideomycetes"},{"taxid":715962,"rank":"clade","names":{"dothideomyceta":"scientific_name"},"parentid":716546,"name":"dothideomyceta"},{"taxid":716546,"rank":"clade","names":{"leotiomyceta":"scientific_name"},"parentid":147538,"name":"leotiomyceta"},{"taxid":147538,"rank":"subphylum","names":{"Pezizomycotina":"scientific_name"},"parentid":716545,"name":"Pezizomycotina"},{"taxid":716545,"rank":"clade","names":{"saccharomyceta":"scientific_name"},"parentid":4890,"name":"saccharomyceta"},{"taxid":4890,"rank":"phylum","names":{"Ascomycota":"scientific_name"},"parentid":451864,"name":"Ascomycota"},{"taxid":451864,"rank":"subkingdom","names":{"Dikarya":"scientific_name"},"parentid":4751,"name":"Dikarya"},{"taxid":4751,"rank":"kingdom","names":{"Fungi":"scientific_name"},"parentid":33154,"name":"Fungi"},{"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"}]}

$: ncbi-taxonomist map  -a MH842226.1 NQWZ01000003.1 | ncbi-taxonomist resolve -x -m
<resolve><query value="MH842226.1" cast="accession"><accession><taxid>122929</taxid><uid>1476663987</uid><database>nucleotide</database><accessions><accessionversion>MH842226.1</accessionversion><caption>MH842226</caption><extra>gi|1476663987|gb|MH842226.1|</extra></accessions></accession></query><lineage><taxon><taxid>122929</taxid><rank>clade</rank><name>Norovirus GII</name><parentid>11983</parentid><names><name type="scientific_name">Norovirus GII</name><name type="EquivalentName">Norovirus genogroup 2</name><name type="EquivalentName">Norovirus genogroup II</name><name type="EquivalentName">Norwalk-like virus genogroup 2</name><name type="EquivalentName">Norwalk-like viruses genogroup 2</name><name type="EquivalentName">human calicivirus genogroup 2</name></names></taxon><taxon><taxid>11983</taxid><rank>species</rank><name>Norwalk virus</name><parentid>142786</parentid><names><name type="scientific_name">Norwalk virus</name></names></taxon><taxon><taxid>142786</taxid><rank>genus</rank><name>Norovirus</name><parentid>11974</parentid><names><name type="scientific_name">Norovirus</name></names></taxon><taxon><taxid>11974</taxid><rank>family</rank><name>Caliciviridae</name><parentid>464095</parentid><names><name type="scientific_name">Caliciviridae</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>
<resolve><query value="NQWZ01000003.1" cast="accession"><accession><taxid>45151</taxid><uid>1391950314</uid><database>nucleotide</database><accessions><accessionversion>NQWZ01000003.1</accessionversion><caption>NQWZ01000003</caption><extra>gi|1391950314|gb|NQWZ01000003.1||gnl|WGS:NQWZ01|ARCrossB10_scaffold_00003</extra></accessions></accession></query><lineage><taxon><taxid>45151</taxid><rank>species</rank><name>Pyrenophora tritici-repentis</name><parentid>5027</parentid><names><name type="scientific_name">Pyrenophora tritici-repentis</name><name type="Synonym">Drechslera tritici-repentis</name><name type="Synonym">Pyrenophora triticirepentis</name><name type="Includes">Pyrenophora sp. CBS 259.59</name><name type="Includes">Pyrenophora sp. MUCL 18687</name></names></taxon><taxon><taxid>5027</taxid><rank>genus</rank><name>Pyrenophora</name><parentid>28556</parentid><names><name type="scientific_name">Pyrenophora</name></names></taxon><taxon><taxid>28556</taxid><rank>family</rank><name>Pleosporaceae</name><parentid>715340</parentid><names><name type="scientific_name">Pleosporaceae</name></names></taxon><taxon><taxid>715340</taxid><rank>suborder</rank><name>Pleosporineae</name><parentid>92860</parentid><names><name type="scientific_name">Pleosporineae</name></names></taxon><taxon><taxid>92860</taxid><rank>order</rank><name>Pleosporales</name><parentid>451868</parentid><names><name type="scientific_name">Pleosporales</name></names></taxon><taxon><taxid>451868</taxid><rank>subclass</rank><name>Pleosporomycetidae</name><parentid>147541</parentid><names><name type="scientific_name">Pleosporomycetidae</name></names></taxon><taxon><taxid>147541</taxid><rank>class</rank><name>Dothideomycetes</name><parentid>715962</parentid><names><name type="scientific_name">Dothideomycetes</name></names></taxon><taxon><taxid>715962</taxid><rank>clade</rank><name>dothideomyceta</name><parentid>716546</parentid><names><name type="scientific_name">dothideomyceta</name></names></taxon><taxon><taxid>716546</taxid><rank>clade</rank><name>leotiomyceta</name><parentid>147538</parentid><names><name type="scientific_name">leotiomyceta</name></names></taxon><taxon><taxid>147538</taxid><rank>subphylum</rank><name>Pezizomycotina</name><parentid>716545</parentid><names><name type="scientific_name">Pezizomycotina</name></names></taxon><taxon><taxid>716545</taxid><rank>clade</rank><name>saccharomyceta</name><parentid>4890</parentid><names><name type="scientific_name">saccharomyceta</name></names></taxon><taxon><taxid>4890</taxid><rank>phylum</rank><name>Ascomycota</name><parentid>451864</parentid><names><name type="scientific_name">Ascomycota</name></names></taxon><taxon><taxid>451864</taxid><rank>subkingdom</rank><name>Dikarya</name><parentid>4751</parentid><names><name type="scientific_name">Dikarya</name></names></taxon><taxon><taxid>4751</taxid><rank>kingdom</rank><name>Fungi</name><parentid>33154</parentid><names><name type="scientific_name">Fungi</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>
```

### Collect taxa remotely

Collect taxid and names remotely, mainly to collect taxonomic data to store in
local database. Does not work on local database.

#### Collect taxid and names remotely

```
$ ncbi-taxonomist collect -t 562,10508  -n man, 'Influenza B virus (B/Acre/121609/2012)'
{"taxid":10239,"rank":"superkingdom","names":{"Viruses":"scientific_name"},"parentid":null,"name":"Viruses"}
{"taxid":2559587,"rank":"clade","names":{"Riboviria":"scientific_name"},"parentid":10239,"name":"Riboviria"}
{"taxid":2732396,"rank":"kingdom","names":{"Orthornavirae":"scientific_name"},"parentid":2559587,"name":"Orthornavirae"}
{"taxid":2497569,"rank":"phylum","names":{"Negarnaviricota":"scientific_name"},"parentid":2732396,"name":"Negarnaviricota"}
{"taxid":2497571,"rank":"subphylum","names":{"Polyploviricotina":"scientific_name"},"parentid":2497569,"name":"Polyploviricotina"}
{"taxid":2497577,"rank":"class","names":{"Insthoviricetes":"scientific_name"},"parentid":2497571,"name":"Insthoviricetes"}
{"taxid":2499411,"rank":"order","names":{"Articulavirales":"scientific_name"},"parentid":2497577,"name":"Articulavirales"}
{"taxid":11308,"rank":"family","names":{"Orthomyxoviridae":"scientific_name"},"parentid":2499411,"name":"Orthomyxoviridae"}
{"taxid":197912,"rank":"genus","names":{"Betainfluenzavirus":"scientific_name"},"parentid":11308,"name":"Betainfluenzavirus"}
{"taxid":11520,"rank":"species","names":{"Influenza B virus":"scientific_name"},"parentid":197912,"name":"Influenza B virus"}
#cut
```

### Piping `ncbi-taxonomist`

An example showing the individual steps and outputs to collect remote
taxonomies, store them in local database, and resolve the lineages. The last
point shows how to  use  pipes to create e small taxonomic pipeline.

#### 1. Collect taxa information remotely and import into local database `taxa.db`

```
$ ncbi-taxonomist collect -t 562,10508 -n man, 'Influenza B virus (B/Acre/121609/2012)' | ncbi-taxonomist import --database taxa.db
{"taxid":10239,"rank":"superkingdom","names":{"Viruses":"scientific_name"},"parentid":null,"name":"Viruses"}
{"taxid":2559587,"rank":"clade","names":{"Riboviria":"scientific_name"},"parentid":10239,"name":"Riboviria"}
{"taxid":2732396,"rank":"kingdom","names":{"Orthornavirae":"scientific_name"},"parentid":2559587,"name":"Orthornavirae"}
{"taxid":2497569,"rank":"phylum","names":{"Negarnaviricota":"scientific_name"},"parentid":2732396,"name":"Negarnaviricota"}
{"taxid":2497571,"rank":"subphylum","names":{"Polyploviricotina":"scientific_name"},"parentid":2497569,"name":"Polyploviricotina"}
{"taxid":2497577,"rank":"class","names":{"Insthoviricetes":"scientific_name"},"parentid":2497571,"name":"Insthoviricetes"}
#cut
```

##### 2. Test local database:

`$ sqlite3 -line taxa.db  'SELECT * FROM taxa;SELECT * FROM names;`

##### 3. Resolve lineages from local database:

```
$ ncbi-taxonomist resolve -t 562,10508  -n man, 'Influenza B virus' -db taxa.db

{"mode":"resolve","query":"Influenza B virus","cast":"taxon","taxon":{"taxid":11520,"rank":"species","names":{"Influenza B virus":"scientific_name"},"parentid":197912,"name":"Influenza B virus"},"lineage":[{"taxid":11520,"rank":"species","names":{"Influenza B virus":"scientific_name"},"parentid":197912,"name":"Influenza B virus"},{"taxid":197912,"rank":"genus","names":{"Betainfluenzavirus":"scientific_name"},"parentid":11308,"name":"Betainfluenzavirus"},{"taxid":11308,"rank":"family","names":{"Orthomyxoviridae":"scientific_name"},"parentid":2499411,"name":"Orthomyxoviridae"},{"taxid":2499411,"rank":"order","names":{"Articulavirales":"scientific_name"},"parentid":2497577,"name":"Articulavirales"},{"taxid":2497577,"rank":"class","names":{"Insthoviricetes":"scientific_name"},"parentid":2497571,"name":"Insthoviricetes"},{"taxid":2497571,"rank":"subphylum","names":{"Polyploviricotina":"scientific_name"},"parentid":2497569,"name":"Polyploviricotina"},{"taxid":2497569,"rank":"phylum","names":{"Negarnaviricota":"scientific_name"},"parentid":2732396,"name":"Negarnaviricota"},{"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"}]}
{"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":"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"},"lineage":[{"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"},{"taxid":561,"rank":"genus","names":{"Escherichia":"scientific_name"},"parentid":543,"name":"Escherichia"},{"taxid":543,"rank":"family","names":{"Enterobacteriaceae":"scientific_name"},"parentid":91347,"name":"Enterobacteriaceae"},{"taxid":91347,"rank":"order","names":{"Enterobacterales":"scientific_name"},"parentid":1236,"name":"Enterobacterales"},{"taxid":1236,"rank":"class","names":{"Gammaproteobacteria":"scientific_name"},"parentid":1224,"name":"Gammaproteobacteria"},{"taxid":1224,"rank":"phylum","names":{"Proteobacteria":"scientific_name"},"parentid":2,"name":"Proteobacteria"},{"taxid":2,"rank":"superkingdom","names":{"Bacteria":"scientific_name"},"parentid":131567,"name":"Bacteria"},{"taxid":131567,"rank":"no rank","names":{"cellular organisms":"scientific_name"},"parentid":null,"name":"cellular organisms"}]}
{"mode":"resolve","query":"10508","cast":"taxon","taxon":{"taxid":10508,"rank":"family","names":{"Adenoviridae":"scientific_name"},"parentid":2732559,"name":"Adenoviridae"},"lineage":[{"taxid":10508,"rank":"family","names":{"Adenoviridae":"scientific_name"},"parentid":2732559,"name":"Adenoviridae"},{"taxid":2732559,"rank":"order","names":{"Rowavirales":"scientific_name"},"parentid":2732529,"name":"Rowavirales"},{"taxid":2732529,"rank":"class","names":{"Tectiliviricetes":"scientific_name"},"parentid":2732008,"name":"Tectiliviricetes"},{"taxid":2732008,"rank":"phylum","names":{"Preplasmiviricota":"scientific_name"},"parentid":2732005,"name":"Preplasmiviricota"},{"taxid":2732005,"rank":"kingdom","names":{"Bamfordvirae":"scientific_name"},"parentid":2732004,"name":"Bamfordvirae"},{"taxid":2732004,"rank":"clade","names":{"Varidnaviria":"scientific_name"},"parentid":10239,"name":"Varidnaviria"},{"taxid":10239,"rank":"superkingdom","names":{"Viruses":"scientific_name"},"parentid":null,"name":"Viruses"}]}
```

##### 4. All in one go and report in XML

```
$ ncbi-taxonomist collect -t 562,10508  -n man, 'Influenza B virus (B/Acre/121609/2012)' |  ncbi-taxonomist import -db taxa.db  | ncbi-taxonomist resolve -x
<resolve><query value="1334390" cast="taxid"><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></query><lineage><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><taxon><taxid>11520</taxid><rank>species</rank><name>Influenza B virus</name><parentid>197912</parentid><names><name type="scientific_name">Influenza B virus</name></names></taxon><taxon><taxid>197912</taxid><rank>genus</rank><name>Betainfluenzavirus</name><parentid>11308</parentid><names><name type="scientific_name">Betainfluenzavirus</name></names></taxon><taxon><taxid>11308</taxid><rank>family</rank><name>Orthomyxoviridae</name><parentid>2499411</parentid><names><name type="scientific_name">Orthomyxoviridae</name></names></taxon><taxon><taxid>2499411</taxid><rank>order</rank><name>Articulavirales</name><parentid>2497577</parentid><names><name type="scientific_name">Articulavirales</name></names></taxon><taxon><taxid>2497577</taxid><rank>class</rank><name>Insthoviricetes</name><parentid>2497571</parentid><names><name type="scientific_name">Insthoviricetes</name></names></taxon><taxon><taxid>2497571</taxid><rank>subphylum</rank><name>Polyploviricotina</name><parentid>2497569</parentid><names><name type="scientific_name">Polyploviricotina</name></names></taxon><taxon><taxid>2497569</taxid><rank>phylum</rank><name>Negarnaviricota</name><parentid>2732396</parentid><names><name type="scientific_name">Negarnaviricota</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>
<resolve><query value="9606" cast="taxid"><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="562" cast="taxid"><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></query><lineage><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><taxon><taxid>561</taxid><rank>genus</rank><name>Escherichia</name><parentid>543</parentid><names><name type="scientific_name">Escherichia</name></names></taxon><taxon><taxid>543</taxid><rank>family</rank><name>Enterobacteriaceae</name><parentid>91347</parentid><names><name type="scientific_name">Enterobacteriaceae</name></names></taxon><taxon><taxid>91347</taxid><rank>order</rank><name>Enterobacterales</name><parentid>1236</parentid><names><name type="scientific_name">Enterobacterales</name></names></taxon><taxon><taxid>1236</taxid><rank>class</rank><name>Gammaproteobacteria</name><parentid>1224</parentid><names><name type="scientific_name">Gammaproteobacteria</name></names></taxon><taxon><taxid>1224</taxid><rank>phylum</rank><name>Proteobacteria</name><parentid>2</parentid><names><name type="scientific_name">Proteobacteria</name></names></taxon><taxon><taxid>2</taxid><rank>superkingdom</rank><name>Bacteria</name><parentid>131567</parentid><names><name type="scientific_name">Bacteria</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="10508" cast="taxid"><taxon><taxid>10508</taxid><rank>family</rank><name>Adenoviridae</name><parentid>2732559</parentid><names><name type="scientific_name">Adenoviridae</name></names></taxon></query><lineage><taxon><taxid>10508</taxid><rank>family</rank><name>Adenoviridae</name><parentid>2732559</parentid><names><name type="scientific_name">Adenoviridae</name></names></taxon><taxon><taxid>2732559</taxid><rank>order</rank><name>Rowavirales</name><parentid>2732529</parentid><names><name type="scientific_name">Rowavirales</name></names></taxon><taxon><taxid>2732529</taxid><rank>class</rank><name>Tectiliviricetes</name><parentid>2732008</parentid><names><name type="scientific_name">Tectiliviricetes</name></names></taxon><taxon><taxid>2732008</taxid><rank>phylum</rank><name>Preplasmiviricota</name><parentid>2732005</parentid><names><name type="scientific_name">Preplasmiviricota</name></names></taxon><taxon><taxid>2732005</taxid><rank>kingdom</rank><name>Bamfordvirae</name><parentid>2732004</parentid><names><name type="scientific_name">Bamfordvirae</name></names></taxon><taxon><taxid>2732004</taxid><rank>clade</rank><name>Varidnaviria</name><parentid>10239</parentid><names><name type="scientific_name">Varidnaviria</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>
```
Please note: this will return taxids, not names, But the lineages are identical.
To keep the names, reuse  `-t 562,10508  -n man, 'Influenza B virus (B/Acre/121609/2012)'`
from the collect step in the last `resolve` step.

### Subtree to extract lineages and ranks

Subtree can extract whole or partial lineages from any taxid within its lineage.
This command works currently only with a local database. This examples creates
local database to demonstrate the command.

#### Creating a local database:

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

#### Obtaining subtrees

```
$ 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"}]}

$ ncbi-taxonomist subtree -x -db test.db -t 142786 9606 --lrank order --hrank phylum
<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>
<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></tree></subtree>
```
### Group

Groups can organize taxa into non-taxonomic groups, e.g. taxa used
in an experiment. The example collects two species by its common name,
stores them in a local database and adds the to the group 'tree'.

```
$ 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
```

### Empty result examples
 map -edb bioproject -a PRJNA604394,PRJNA604390
-> [PRJNA604390](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA604390)has no species data

### Format specific filed from map output to `CSV` and `TSV` using `jq`

Extract  taxid, rank, and scientific name from `map` `JSON` output using `jq`:

```
$: ncbi-taxonomist map -t 2 -n human -r | \
jq -r '[.taxon.taxid,.taxon.rank,(.taxon.names|to_entries[]|select(.value=="scientific_name").key)]|@csv'
9606,"species","Homo sapiens"
2,"superkingdom","Bacteria"
```
For TSV output, substitute @csv with @tsv in the `jq` command:
```
9606    species Homo sapiens
2       superkingdom    Bacteria
```


