Welcome to the JGI taxonomy server!
This service provides taxonomy information from NCBI taxID numbers, gi numbers, organism names, and accessions.
The output is formatted as a Json object.

Usage:

All addresses below are assumed to be prefixed by https://taxonomy.jgi.doe.gov, e.g. /name/homo_sapiens implies a full URL of:
https://taxonomy.jgi.doe.gov/name/homo_sapiens

/name/homo_sapiens will give taxonomy information for an organism name.
Names are case-insensitive and underscores are equivalent to spaces.
/id/9606 will give taxonomy information for an NCBI taxID.
/gi/1234 will give taxonomy information from an NCBI gi number.
/accession/NZ_AAAA01000057.1 will give taxonomy information from an accession.
/header/ will accept an NCBI sequence header such as gi|7|emb|X51700.1| Bos taurus
/silvaheader/ will accept a Silva sequence header such as KC415233.1.1497 Bacteria;Spirochaetae;Spirochaetes
/img/ will accept an IMG id such as 2724679250
Vertical bars (|) may cause problems on the command line and can be replaced by tilde (~).

Comma-delimited lists are accepted for bulk queries, such as tax/gi/1234,7000,42
For plaintext (non-Json) results, add the term /pt/ or /sc/.
pt will give just the taxID, while sc will give the whole lineage, semicolon-delimited. For example:
/pt/name/homo_sapiens
/sc/gi/1234

Additional supported display options are children, numchildren, range, simple, path, size, and ancestor.
The order is not important but they need to come before the query term.  For example:
/children/numchildren/range/gi/1234

To find the common ancestor of multiple organisms, add /ancestor/. For example:
/id/ancestor/1234,5678,42
/name/ancestor/homo_sapiens,canis_lupus,bos_taurus

For a simplified taxonomic tree, add simple.
This will ignore unranked or uncommon levels like tribe and parvorder, and only display the following levels:
SUBSPECIES, SPECIES, GENUS, FAMILY, ORDER, CLASS, PHYLUM, KINGDOM, SUPERKINGDOM, DOMAIN
For example:
/simple/id/1234

To print taxonomy from the command line in Linux, use curl:
curl https://taxonomy.jgi.doe.gov/id/9606

Queries longer than around 8kB can be sent via POST: curl https://taxonomy..doe.gov/POST
...where the data sent is, for example: name/e.coli,h.sapiens,c.lupus

Last restarted Tue Dec 10 14:06:02 PST 2024
Running BBMap version 38.97


Queries:   5005964
Usage:     705450
Avg time:  1.131 ms
Last time: 0.128 ms
Avg time:  0.207 ms (usage queries)
Last time: 0.186 ms (usage queries)

Internal:  5005964
External:  0
NotFound:  72335

gi:        1173
Name:      6042
TaxID:     4929399
Header:    6392
Accession: 61601
IMG:       40
Silva:     1317

Simple:    10784
Ancestor:  22
Children:  0

Json:      4914037
Plaintext: 52816
Semicolon: 39111
Path:      0
Size:      0
Single:    4973162
Bulk:      51282
Total:     997955209