pyinaturalist 0.14.0b2

iNaturalist API client for python

pyinaturalist

Introduction

iNaturalist is a community science platform that helps people get involved in the natural world by observing and identifying the living things around them. Collectively, the community produces a rich source of global biodiversity data that can be valuable to anyone from hobbyists to scientists.

pyinaturalist is an unofficial client for the iNaturalist API that aims to make these data easily accessible in the python programming language.

• Features
• Quickstart
• Next Steps
• Feedback
• Related Projects

Features

• Easier requests: Complete type annotations for request parameters, and simplified create/update request formats
• Convenient responses: Type conversions to the things you would expect in python
• Docs: Example requests, responses, scripts, and Jupyter notebooks to help get you started
• Security: Keyring integration for secure credential storage
• Server-friendly: Client-side rate-limiting that follows the API Recommended Practices, so you can be nice to the iNaturalist servers and not worry about rate-limiting errors
• Test-friendly: A dry-run mode to preview your requests before potentially modifying data

Many of the most relevant API endpoints are included, and more are on the way:

• Searching for:
  • controlled terms
  • identifications
  • observations (multiple formats)
  • observation fields
  • observation species counts
  • places
  • projects
  • species
• Text search autocompletion for:
  • places
  • species
  • users
• Creating and updating:
  • observations
  • observation fields
  • observation photos
  • observation sounds

Quickstart

Here are usage examples for some of the most commonly used features.

First, install with pip:

pip install pyinaturalist

Then, import the main API functions:

from pyinaturalist import *

Search observations

Let's start by searching for all your own observations. There are numerous fields you can search on, but we'll just use user_id for now:

>>> observations = get_observations(user_id='my_username')

The full response will be in JSON format, but we can just print out a few basic details:

>>> for obs in observations['results']:
>>>    print(format_observations(obs))
[78242978] Species: Agelastica alni (Alder Leaf Beetle) observed by niconoe on 2021-05-10 18:45:38+01:00 at 1428 Braine-l'Alleud, Belgique
[78218860] Genus: Bradybatus observed by niconoe on 2021-05-10 15:22:49+01:00 at 1428 Braine-l'Alleud, Belgique
...

You can also get observation counts by species. On iNaturalist.org, this information can be found on the 'Species' tab of search results. For example, to get the counts of all your own research-grade observations:

>>> counts = get_observation_species_counts(user_id='my_username', quality_grade='research')
>>> print(format_species_counts(counts, align=True))
[48473   ]: Species:          Ganoderma applanatum (Artist's bracket): 4
[50310   ]: Species:         Arisaema triphyllum (Jack-in-the-pulpit): 4
[50817   ]:   Genus:                     Auricularia (Wood ear fungi): 3
[81599   ]: Species:                 Silphium perfoliatum (Cup plant): 3
[120215  ]: Species:    Bombus griseocollis (Brown-belted Bumble Bee): 2
...

Another useful format is the observation histogram, which shows the number of observations over a given interval. The default is month_of_year:

>>> histogram = get_observation_histogram(user_id='my_username')
>>> print(histogram)
{
    1: 8,  # January
    2: 1,  # February
    3: 19, # March
    ...,   # etc.
}

Create and update observations

To create or modify observations, you will first need to log in. This requires creating an iNaturalist app, which will be used to get an access token.

token = get_access_token(
    username='my_username',
    password='my_password',
    app_id='my_app_id',
    app_secret='my_app_secret',
)

See Authentication for additional authentication options, including environment variables, keyrings, and password managers.

Now we can create a new observation:

from datetime import datetime

response = create_observation(
    taxon_id=54327,  # Vespa Crabro
    observed_on_string=datetime.now(),
    time_zone='Brussels',
    description='This is a free text comment for the observation',
    tag_list='wasp, Belgium',
    latitude=50.647143,
    longitude=4.360216,
    positional_accuracy=50, # GPS accuracy in meters
    access_token=token,
    photos=['~/observations/wasp1.jpg', '~/observations/wasp2.jpg']
)

# Save the new observation ID
new_observation_id = response[0]['id']

We can then update the observation information, photos, or sounds:

update_observation(
    17932425,
    access_token=token,
    description='updated description !',
    photos='~/observations/wasp_nest.jpg',
    sounds='~/observations/wasp_nest.mp3',
)

Search species

Let's say you partially remember either a genus or family name that started with 'vespi'-something. The taxa endpoint can be used to search by name, rank, and several other criteria

>>> response = get_taxa(q='vespi', rank=['genus', 'family'])

As with observations, there is a lot of information in the response, but we'll print just a few basic details:

>>> print(format_taxa(response))
[52747] Family: Vespidae (Hornets, Paper Wasps, Potter Wasps, and Allies)
[92786] Genus: Vespicula
[84737] Genus: Vespina
...

Oh, that's right, it was 'Vespidae'! Now let's find all of its subfamilies using its taxon ID from the results above:

>>> response = get_taxa(parent_id=52747)
>>> print(format_taxa(response))
[343248] Subfamily: Polistinae (Paper Wasps)
[ 84738] Subfamily: Vespinae (Hornets and Yellowjackets)
[119344] Subfamily: Eumeninae (Potter and Mason Wasps)
...

Just one last example. There is a taxon autocomplete text search endpoint, which is a bit more niche, and is intended for autocomplete interfaces like the one on iNaturalist.org:

But it also provides an easy way to search the iNaturalist taxonomy database by taxon name. Here is a quick example that will run searches from console input:

while True:
    query = input("> ")
    response = get_taxa_autocomplete(q=query)
    print(format_taxa(response, align=True))

Example usage:

> opilio
[  527573]        Genus                                              Opilio
[   47367]        Order                              Opiliones (Harvestmen)
[   84644]      Species             Phalangium opilio (European Harvestman)
...
> coleo
[  372759]     Subclass     Coleoidea (Octopuses, Squids, and Cuttlefishes)
[   47208]        Order                                Coleoptera (Beetles)
[  359229]      Species  Coleotechnites florae (Coleotechnites Flower Moth)
...
<Ctrl-C>

Next Steps

For more information, see:

• User Guide: introduction and general features that apply to most endpoints
• Endpoint Summary: a complete list of endpoints wrapped by pyinaturalist
• Examples: data visualizations and other examples of things to do with iNaturalist data
• Reference: Detailed API documentation
• Contributing Guide: development details for anyone interested in contributing to pyinaturalist
• History: details on past and current releases
• Issues: planned & proposed features

Feedback

If you have any problems, suggestions, or questions about pyinaturalist, please let us know! Just create an issue. Also, PRs are welcome!

Note: pyinaturalist is developed by members of the iNaturalist community, and is not endorsed by iNaturalist.org or the California Academy of Sciences. If you have non-python-specific questions about iNaturalist, the iNaturalist Community Forum is the best place to start.

Related Projects

• pyinaturalist-open-data: Tools for working with iNaturalist open data
• pyinaturalist-notebook: Jupyter notebook Docker image for pyinaturalist
• pyinaturalist-convert: (WIP) Tools to convert observation data to and from multiple formats