pygbif

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Python client for the GBIF API <https://www.gbif.org/developer/summary>_

Source on GitHub at sckott/pygbif <https://github.com/sckott/pygbif>_

Other GBIF clients:

  • R: rgbif, ropensci/rgbif <https://github.com/ropensci/rgbif>_
  • Ruby: gbifrb, sckott/gbifrb <https://github.com/sckott/gbifrb>_

Installation

Stable from pypi

.. code-block:: console

pip install pygbif

Development version

.. code-block:: console

[sudo] pip install git+git://github.com/sckott/pygbif.git#egg=pygbif

pygbif is split up into modules for each of the major groups of API methods.

  • Registry - Datasets, Nodes, Installations, Networks, Organizations
  • Species - Taxonomic names
  • Occurrences - Occurrence data, including the download API
  • Maps - Maps, get raster maps from GBIF as png or mvt

You can import the entire library, or each module individually as needed.

In addition there is a utils module, currently with one method: wkt_rewind, and a caching method to manage whether HTTP requests are cached or not. See ?pygbif.caching.

Registry module

registry module API:

  • organizations
  • nodes
  • networks
  • installations
  • datasets
  • dataset_metrics
  • dataset_suggest
  • dataset_search

Example usage:

.. code-block:: python

from pygbif import registry
registry.dataset_metrics(uuid='3f8a1297-3259-4700-91fc-acc4170b27ce')

Species module

species module API:

  • name_backbone
  • name_suggest
  • name_usage
  • name_lookup
  • name_parser

Example usage:

.. code-block:: python

from pygbif import species
species.name_suggest(q='Puma concolor')

Occurrences module

registry module API:

  • search
  • get
  • get_verbatim
  • get_fragment
  • count
  • count_basisofrecord
  • count_year
  • count_datasets
  • count_countries
  • count_schema
  • count_publishingcountries
  • download
  • download_meta
  • download_list
  • download_get

Example usage:

.. code-block:: python

from pygbif import occurrences as occ
occ.search(taxonKey = 3329049)
occ.get(key = 252408386)
occ.count(isGeoreferenced = True)
occ.download('basisOfRecord = LITERATURE')
occ.download('taxonKey = 3119195')
occ.download('decimalLatitude > 50')
occ.download_list(user = "sckott", limit = 5)
occ.download_meta(key = "0000099-140929101555934")
occ.download_get("0000066-140928181241064")

Maps module

maps module API:

  • map

Example usage:

.. code-block:: python

from pygbif import maps
out = maps.map(taxonKey = 212, year = 1998, bin = "hex",
       hexPerTile = 30, style = "classic-noborder.poly")
out.response
out.path
out.img
out.plot()

.. image:: https://github.com/sckott/pygbif/raw/master/gbif_map.png :width: 25% :scale: 25%

utils module

utils module API:

  • wkt_rewind

Example usage:

.. code-block:: python

from pygbif import utils
x = 'POLYGON((144.6 13.2, 144.6 13.6, 144.9 13.6, 144.9 13.2, 144.6 13.2))'
utils.wkt_rewind(x)

Contributors

  • Scott Chamberlain <https://github.com/sckott>_
  • Robert Forkel <https://github.com/xrotwang>_
  • Jan Legind <https://github.com/jlegind>_
  • Stijn Van Hoey <https://github.com/stijnvanhoey>_
  • Peter Desmet <https://github.com/peterdesmet>_
  • Nicolas Noé <https://github.com/niconoe>_

Meta

  • License: MIT, see LICENSE file <LICENSE>_
  • Please note that this project is released with a Contributor Code of Conduct <CONDUCT.md>_. By participating in this project you agree to abide by its terms.

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Pygbif

GBIF Python client

Pygbif Info

⭐ Stars 30
🔗 Homepage pygbif.readthedocs.io
🔗 Source Code github.com
🕒 Last Update a year ago
🕒 Created 7 years ago
🐞 Open Issues 15
➗ Star-Issue Ratio 2
😎 Author sckott