pypi docs travis coverage black

This is a port of the R package taxize. There is a lot going on in the R version of this library, so it will take a while to get all the same functionality over here.

Why? A significant advantage of a Python version of taxize will be for those that are pythonistas at heart. Also, you could use pytaxize in a web app, whereas you could with taxize (e.g., in a Shiny app), but it wouldn’t scale, be very fast, etc.


Stable from pypi

pip install pytaxize

Development version

sudo pip install git+git://

Taxonomic Ids

I’ve started working on a class interface for taxonomic IDs, which will have a bunch of extension methods to do various things with taxon ids. What’s available right now is just getting COL ids.

from pytaxize import Ids
res = Ids('Poa annua')
{'Poa annua': [{'id': '93036',
   'name': 'Poa annua',
   'rank': 'species',
   'uri': ''}]}


from pytaxize import itis

{'acceptedName': 'Dasiphora fruticosa',
   'acceptedTsn': '836659',
   'author': '(L.) Rydb.'}
itis.hierarchy_up(tsn = 36485)

{'author': 'Raf.',
 'parentName': 'Asteraceae',
 'parentTsn': '35420',
 'rankName': 'Genus',
 'taxonName': 'Agoseris',
 'tsn': '36485'}

Catalogue of Life

from pytaxize import col
x = col.children(name=["Apis"])
[{'id': '7a4a38c5095963949d6d6ec917d471de',
  'name': 'Apis andreniformis',
  'rank': 'Species'},
 {'id': '39610a4ceff7e5244e334a3fbc5e47e5',
  'name': 'Apis cerana',
  'rank': 'Species'}]


pytaxize modules
Introduction to pygbif modules.
Taxonomic Identifiers Class
The Ids class
Scientific and common names
Scientific to common names, and vice versa
The ncbi module: NCBI methods
The itis module: ITIS methods
Global Names Resolver
The gn module: methods for Global Names Index and Resolver
Global Biodiversity Information Facility
The gbif module: GBIF methods
Catalogue of Life
The col module: Catalogue of Life methods
Other methods
Variety of other methods

All the rest

See what has changed in recent pygbif versions.
pygbif contributors.
Learn how to contribute to the pygbif project.
Contributor Code of Conduct
Expected behavior in this community. By participating in this project you agree to abide by its terms.
The pygbif license.

Indices and tables