pyinaturalist

Pyinaturalist is an iNaturalist API client for python.

Features

iNaturalist offers a rich source of biodiversity data, and an extensive API to interact with it. If you want to make use of these data in python, then pyinaturalist can help! It adds a number of python-specific conveniences, including:

  • Requests: Simplified usage with python types and data structures
  • Responses: Type conversions to things you would expect in python
  • Server-Friendly Usage: Client-side rate-limiting that follows the API Recommended Practices
  • Typing: Complete type annotations for request parameters which significantly enhances usability within an IDE, Jupyter notebook, or any other environment with type checking & autocompletion
  • Docs: Thorough documentation with example requests and responses
  • Security: Keyring integration for secure credential storage
  • Testing: A dry-run mode to preview your requests before potentially modifying data

Many of the most relevant API endpoints are included:

  • 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

Quickstart

Following 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,
)

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

Next we can upload a picture for this observation:

add_photo_to_observation(
    new_observation_id,
    access_token=token,
    photo='/Users/nicolasnoe/vespa.jpg',
)

And then update the observation:

update_observation(
    17932425,
    access_token=token,
    description='updated description !',
)

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:

pyinaturalist-1

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)
...
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