pygbif

Making the data of the Global Biodiversity Information Facility API accessible via Python.
https://github.com/gbif/pygbif

Category: Biosphere
Sub Category: Biodiversity Data Access and Management

Keywords

api biodiversity data ecology gbif

Keywords from Contributors

lifewatch oscibio taxonomy biodiversity-informatics weather occurrence species jekyll reporter climate

Last synced: about 16 hours ago
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Repository metadata

GBIF Python client

• Host: GitHub
• URL: https://github.com/gbif/pygbif
• Owner: gbif
• License: mit
• Created: 2014-12-31T05:36:27.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2024-12-02T09:58:18.000Z (5 months ago)
• Last Synced: 2025-04-25T14:44:03.258Z (1 day ago)
• Topics: api, biodiversity, data, ecology, gbif
• Language: Python
• Homepage: https://pygbif.readthedocs.io/en/latest/
• Size: 20.5 MB
• Stars: 127
• Watchers: 18
• Forks: 32
• Open Issues: 31
• Releases: 12
• Metadata Files:
  • Readme: README.rst
  • Changelog: Changelog.rst
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE

README.rst

          pygbif
======

|pypi| |docs| |ghactions| |coverage| |black|

Python client for the `GBIF API `_

`Source on GitHub at gbif/pygbif `_

Other GBIF clients:

* R: `rgbif`, `ropensci/rgbif `_
* Ruby: `gbifrb`, `sckott/gbifrb `_
* PHP: `php-gbif`, `restelae/php-gbif `_

Contributing: `CONTRIBUTING.md `_

Installation
============

Stable from pypi

.. code-block:: console

    pip install pygbif

Development version

.. code-block:: console

    [sudo] pip install git+git://github.com/gbif/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
==================

occurrences 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`
* `download_citation`
* `download_describe`
* `download_sql`

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 = PRESERVED_SPECIMEN')
    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")
    occ.download_citation("0002526-241107131044228")
    occ.download_describe("simpleCsv")
    occ.download_sql("SELECT gbifid,countryCode FROM occurrence WHERE genusKey = 2435098")

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/gbif/pygbif/raw/master/gbif_map.png
   :width: 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 `_
* `Robert Forkel `_
* `Jan Legind `_
* `Stijn Van Hoey `_
* `Peter Desmet `_
* `Nicolas Noé `_

Meta
====

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

.. |pypi| image:: https://img.shields.io/pypi/v/pygbif.svg
   :target: https://pypi.python.org/pypi/pygbif

.. |docs| image:: https://readthedocs.org/projects/pygbif/badge/?version=latest
   :target: http://pygbif.rtfd.org/

.. |ghactions| image:: https://github.com/gbif/pygbif/workflows/Python/badge.svg
   :target: https://github.com/gbif/pygbif/actions?query=workflow%3APython

.. |coverage| image:: https://codecov.io/gh/gbif/pygbif/branch/master/graph/badge.svg?token=frXPREGk1D
   :target: https://codecov.io/gh/gbif/pygbif

.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
   :target: https://github.com/psf/black



        

---

Owner metadata

• Name: Global Biodiversity Information Facility
• Login: gbif
• Email:
• Kind: organization
• Description:
• Website: https://www.gbif.org
• Location: Copenhagen, Denmark
• Twitter:
• Company:
• Icon url: https://avatars.githubusercontent.com/u/1963797?v=4
• Repositories: 288
• Last ynced at: 2024-04-14T06:45:04.085Z
• Profile URL: https://github.com/gbif

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GitHub Events

Total

• Create event: 4
• Release event: 1
• Issues event: 4
• Watch event: 14
• Delete event: 6
• Issue comment event: 5
• Push event: 8
• Pull request review comment event: 3
• Pull request review event: 5
• Pull request event: 5
• Fork event: 4

Last Year

• Create event: 4
• Release event: 1
• Issues event: 4
• Watch event: 14
• Delete event: 6
• Issue comment event: 5
• Push event: 8
• Pull request review comment event: 3
• Pull request review event: 5
• Pull request event: 5
• Fork event: 4

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Committers metadata

Last synced: 6 days ago

Name	Email	Commits
Scott Chamberlain	m****s@g****m	200
Cecilie Svenningsen	5****e	31
stijnvanhoey	s****y@g****m	15
John Waller	j****r@g****m	10
Matthew Blissett	m****t@g****g	8
Nicolas Noé	n****e@i****e	7
John Waller	f****2@k****k	4
Marie Grosjean	m****n@g****g	4
Peter Desmet	p****k@g****m	4
Daniel Lusk	d****k@p****t	1
Keenan Ganz	3****z	1
Ryan Vandersmith	r****h@g****m	1
dependabot-preview[bot]	2****]	1
lucbettaieb	l****b@g****m	1
gbifnorway	g****t@n****o	1
Fabian-Robert Stöter	f****r@i****r	1
marcowyzajomc	1****c	1
xrotwang	x****g@g****m	1

Committer domains:

• gbif.org: 2
• inria.fr: 1
• nhm.uio.no: 1
• posteo.net: 1
• ku.dk: 1
• inbo.be: 1

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Issue and Pull Request metadata

Last synced: 1 day ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/gbif/pygbif

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Package metadata

• Total packages: 1
• Total downloads:
  • pypi: 6,749 last-month
• Total docker downloads: 8,425
• Total dependent packages: 3
• Total dependent repositories: 24
• Total versions: 14
• Total maintainers: 2

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Dependencies

Score: 17.582675176176473