Anatomical reference API endpoint

Immutable, system-managed anatomical atlas release metadata.

Table of contents

1. Endpoints
2. Fields
3. List
4. Detail
5. Writing
6. Data model

Endpoints

• Private portal: https://www.brainstem.org/api/private/taxonomies/anatomicalreference/ (needs a token; one record: append <id>/)
• Public portal: https://www.brainstem.org/api/public/taxonomies/anatomicalreference/ (read-only, public projects, no token)
• Response keys: anatomical_reference (detail, create, update), anatomical_references (list)
• Permissions: see the permissions page
• Uniqueness: code unique across BrainSTEM
• Deleting: refused (400) while anatomicalregion, coordinatetransform, procedure records point to it

Fields

[required] fields must be sent on create; [read-only] fields are returned but cannot be set. A nestable relation can be traversed in filters (filter{field.other}) and sideloaded with include[]=field.*; other relations can only be compared with ids (filter{field}=<id>). See the query syntax.

Field	Description
id	UUID string [read-only]
code	string [read-only]
name	string [read-only]
version	string [read-only]
species	species id [read-only]; nullable
organ	one of brain, spinal_cord, whole_body [read-only]
region_atlas_code	string [read-only]
coordinate_space_identifier	string [read-only]
axes_orientation	JSON object [read-only]
native_unit	string [read-only]
source	string [read-only]
homepage	string [read-only]
citation	string [read-only]
license_name	string [read-only]
license_url	string [read-only]
asset_manifest_url	string [read-only]
visualization_status	one of available, metadata_only, disabled [read-only]
is_active	boolean [read-only]

List

• Allowed portals: private, public
• Request method: GET
• URL: https://www.brainstem.org/api/private/taxonomies/anatomicalreference/
• Responses: 200 OK; 401 Not authenticated; 403 Not allowed

Use example (Python API tool)

resp = client.load('anatomicalreference', load_all=True)
records = resp['anatomical_references']

Use example (MATLAB API tool)

resp = client.load('anatomicalreference', 'load_all', true);
records = resp.anatomical_references;

Response example

{
    "anatomical_references": [
        {
            "id": "<id>",
            "code": "",
            "name": "Anatomical reference 1",
            "version": "",
            "species": "<species-id>",
            "organ": "brain",
            "region_atlas_code": "",
            "coordinate_space_identifier": "",
            "axes_orientation": {},
            "native_unit": "",
            "source": "",
            "homepage": "",
            "citation": "",
            "license_name": "",
            "license_url": "",
            "asset_manifest_url": "",
            "visualization_status": "available",
            "is_active": true
        }
    ],
    "meta": {
        "page": 1,
        "per_page": 100,
        "total_results": 1,
        "total_pages": 1
    }
}

Detail

• Allowed portals: private, public
• Request method: GET
• URL: https://www.brainstem.org/api/private/taxonomies/anatomicalreference/<id>/
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (Python API tool)

resp = client.load('anatomicalreference', id='<id>')
record = resp.json()['anatomical_reference']

Use example (MATLAB API tool)

out = client.load('anatomicalreference', 'id', '<id>');
record = out.anatomical_reference;

Response example

{
    "anatomical_reference": {
        "id": "<id>",
        "code": "",
        "name": "Anatomical reference 1",
        "version": "",
        "species": "<species-id>",
        "organ": "brain",
        "region_atlas_code": "",
        "coordinate_space_identifier": "",
        "axes_orientation": {},
        "native_unit": "",
        "source": "",
        "homepage": "",
        "citation": "",
        "license_name": "",
        "license_url": "",
        "asset_manifest_url": "",
        "visualization_status": "available",
        "is_active": true
    }
}

Writing

This resource is maintained by BrainSTEM administrators or system processes and is read-only through the REST API.

Data model

The fields are described for the web forms on the Anatomical reference data model page.