Species API endpoint

Table of contents

1. Fields
2. List view
3. Add
4. Detail
5. Change
6. Delete
7. List approvals
8. Detail approval
9. Accept approval
10. Reject approval

Fields

Field	Description
id	UUID identificator formatted as a string
name	string [required] [max length: 100; must be unique]
description	string [max length: 2000]
rrid	Research Resource Identifier (RRID)
rrid_url	URL to RRID lookup page [read-only]
external_identifiers	JSON object containing external identifier information
comments	string, used when proposing approval changes

Optional fields such as comments can be omitted from list/detail responses when empty.

List view

• Allowed portals: public, private
• Request method: GET
• URL: https://www.brainstem.org/api/private/taxonomies/species
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.load('species')

Response example

{'species': [
    {
        'id': '<id>',
        'name': 'Rat',
        'description': 'Rattus rattus',
        'rrid': None,
        'rrid_url': None,
        'external_identifiers': []
        },
    {
        'id': '<id>',
        'name': 'Red-eared Turtles',
        'description': 'Trachemys scripta elegans',
        'rrid': None,
        'rrid_url': None,
        'external_identifiers': []
    }
]}

Public list responses also include a meta object (pagination/filter metadata).

Add

• Allowed portals: private
• Request method: POST
• URL: https://www.brainstem.org/api/private/taxonomies/species
• Data: JSON dictionary containing at least the required fields.
• Responses: 201 OK; 400 Bad request; 403 Not allowed; 404 Not found

Note: Species submissions go through an approval process.

Use example (using Python API)

resp = client.save("species",  data={
        "name": "MyNewSpecies",
        "description": "",
    }
)

Response example

{'species_approval': {
    'id': '<id>',
    'name': 'MyNewSpecies',
    'description': '',
    'rrid': None,
    'external_identifiers': []}
}

Detail

• Allowed portals: public, private
• Request method: GET
• URL: https://www.brainstem.org/api/private/taxonomies/species/<id>/
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.load('species', id='<id>')

Response example

{'species': {
    'id': '<id>',
    'name': 'MyNewSpecies',
    'description': '',
    'rrid': None,
    'rrid_url': None,
    'external_identifiers': []}
}

Change

• Allowed portals: private
• Request method: PATCH
• URL: https://www.brainstem.org/api/private/taxonomies/species/<id>/
• Data: dictionary containing the fields to be updated
• Responses: 200 OK; 400 Bad request; 403 Not allowed; 404 Not found

Note: Species changes go through an approval process.

Use example (using Python API)

resp = client.save("species", id="<id>", data={"description": "new text"})

Response example

{'species_approval': {
    'id': '<id>',
    'name': 'MyNewSpecies',
    'description': 'new text',
    'rrid': None,
    'external_identifiers': []}
}

Delete

• Allowed portals: private
• Request method: DELETE
• URL: https://www.brainstem.org/api/private/taxonomies/species/<id>/
• Data: None
• Responses: 204 OK; 403 Not allowed; 404 Not found

Note: only administrators can delete Species.

Use example (using Python API)

resp = client.delete("species", id="<id>")

List approvals

• Allowed portals: private
• Request method: GET
• URL: https://www.brainstem.org/api/private/taxonomies/speciesapproval
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.load('speciesapproval')

Response example

{'species_approvals': [
    {
        'id': '<id>',
        'name': 'MyNewSpecies',
        'description': '',
        'rrid': None,
        'external_identifiers': [],
        'instance_id': None,
        'action': 'Add',
        'reviewer': None,
        'status': 'Pending'
    },
    {
        'id': '<id>',
        'name': 'Digimon',
        'description': 'aaa',
        'rrid': None,
        'external_identifiers': [],
        'instance_id': None,
        'action': 'Add',
        'reviewer': 3,
        'status': 'Rejected'
    }
]}

Detail approval

• Allowed portals: private
• Request method: GET
• URL: https://www.brainstem.org/api/private/taxonomies/speciesapproval/<id>/
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.load('speciesapproval', id='<id>')

Response example

{'species_approval': {
    'id': '<id>',
    'name': 'MyNewSpecies',
    'description': '',
    'rrid': None,
    'external_identifiers': [],
    'instance_id': None,
    'action': 'Add',
    'reviewer': None,
    'status': 'Pending'}
}

Accept approval

• Allowed portals: private
• Request method: PATCH
• URL: https://www.brainstem.org/api/private/taxonomies/speciesapproval/<id>/accept/
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.save("speciesapproval", id="<id>", options="accept")

Reject approval

• Allowed portals: private
• Request method: PATCH
• URL: https://www.brainstem.org/api/private/taxonomies/speciesapproval/<id>/reject/
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.save("speciesapproval", id="<id>", options="reject")