pygbif

An interface to the GBIF API for the Python programming language.

pygbif is a Python package that allows searching and retrieving data from GBIF. pygbif wraps Python code around the GBIF API to allow you to talk to GBIF from Python and access metadata, species names, and occurrences.

The main pygbif documentation can be found at https://pygbif.readthedocs.io/.

Installation

Installing the stable version from PyPI

pip install pygbif

Installing the development version

pip install git+git://github.com/gbif/pygbif.git#egg=pygbif

Getting Started

(Based on the example from the documentation.)

First, load the library:

from pygbif import species as species
from pygbif import occurrences as occ

Look up GBIF backbone taxonomic keys from a list of names:

splist = ['Cyanocitta stelleri', 'Junco hyemalis', 'Aix sponsa',
  'Ursus americanus', 'Pinus conorta', 'Poa annuus']
keys = [ species.name_backbone(x)['usageKey'] for x in splist ]

Then, get a count of occurrence records for each taxon, and pull out number of records found for each taxon:

out = [ occ.search(taxonKey = x, limit=0)['count'] for x in keys ]

Make a dict of species names and number of records, sorting in descending order:

x = dict(zip(splist, out))
sorted(x.items(), key=lambda z:z[1], reverse=True)

Citation

Under the terms of the GBIF data user agreement, users who download data agree to cite a DOI. Please see GBIF’s citation guidelines.

Please also cite pygbif.