JGI BBTools Taxonomy Server

# Welcome to the BBTools Taxonomy Server!

This service provides taxonomy information from NCBI taxID numbers, gi numbers, organism names, and accessions.
Vertical bars (|) may cause problems on the command line and can be replaced by tilde (~).

- /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

## Benefits of using the BBTools Taxonomy Server

- Identifies all intermediate stages of taxonomy tree such as order, phylum, tribe, etc.
- Provides the information in json format
- Fast processing
- Allows queries in bulk with lists instead of single query

Examples of Basic Usage

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

- https://taxonomy.jgi-psf.org/name/homo_sapiens

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-psf.org/id/9606

Queries longer than around 8kB can be sent via POST: curl https://taxonomy.jgi-psf.org/POST...where the data sent is, for example:

- name/e.coli,h.sapiens,c.lupus

Examples of Advanced Usage

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

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