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hra-api-spec.yaml
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openapi: 3.0.3
info:
title: HRA-API
description: |
This API provides programmatic access to data registered to the Human Reference Atlas (HRA).
See the [HuBMAP HRA Portal](https://humanatlas.io/) for details.
version: 0.11.0
contact:
name: HuBMAP Help Desk
email: [email protected]
license:
name: MIT License
url: https://spdx.org/licenses/MIT.html
servers:
- description: HRA-API Production
url: https://apps.humanatlas.io/api
- description: HRA-API Staging
url: https://apps.humanatlas.io/api--staging
- description: CCF-API (deprecated) Production
url: https://apps.humanatlas.io/hra-api
- description: Local Server
url: /
security: []
tags:
- name: v1
description: HRA-API v1 Routes
- name: ds-graph
description: Dataset Graph Routes
- name: hra-pop
description: HRApop Routes
externalDocs:
description: API Documentation
url: https://github.com/x-atlas-consortia/hra-api#readme
paths:
/v1/session-token:
post:
summary: Get a session token
operationId: session-token
tags:
- v1
requestBody:
$ref: '#/components/requestBodies/SessionToken'
responses:
'200':
$ref: '#/components/responses/SessionToken'
'404':
$ref: '#/components/responses/ErrorMessage'
'405':
$ref: '#/components/responses/ErrorMessage'
/v1/db-status:
get:
summary: Get current status of database
operationId: db-status
tags:
- v1
parameters:
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/DatabaseStatus'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/sparql:
get:
summary: Run a SPARQL query
operationId: sparql
tags:
- v1
parameters:
- $ref: '#/components/parameters/Query'
- $ref: '#/components/parameters/Token'
- $ref: '#/components/parameters/Format'
responses:
'200':
$ref: '#/components/responses/SparqlResponse'
'404':
$ref: '#/components/responses/ErrorMessage'
post:
summary: Run a SPARQL query (POST)
operationId: sparql-post
tags:
- v1
requestBody:
$ref: '#/components/requestBodies/SparqlQuery'
parameters:
- $ref: '#/components/parameters/Token'
- $ref: '#/components/parameters/Format'
responses:
'200':
$ref: '#/components/responses/SparqlResponse'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/aggregate-results:
get:
summary: Get aggregate results / statistics
operationId: aggregate-results
tags:
- v1
parameters:
- $ref: '#/components/parameters/Age'
- $ref: '#/components/parameters/AgeRange'
- $ref: '#/components/parameters/Bmi'
- $ref: '#/components/parameters/BmiRange'
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/OntologyTerms'
- $ref: '#/components/parameters/CellTypeTerms'
- $ref: '#/components/parameters/Consortiums'
- $ref: '#/components/parameters/Providers'
- $ref: '#/components/parameters/Sex'
- $ref: '#/components/parameters/SpatialSearches'
- $ref: '#/components/parameters/Technologies'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/AggregateResults'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/get-spatial-placement:
post:
summary: Given a SpatialEntity already placed relative to a reference SpatialEntity, retrieve a new direct SpatialPlacement to the given SpatialEntity IRI
operationId: get-spatial-placement
tags:
- v1
requestBody:
$ref: '#/components/requestBodies/GetSpatialPlacement'
responses:
'200':
$ref: '#/components/responses/SpatialPlacement'
'404':
$ref: '#/components/responses/ErrorMessage'
'500':
$ref: '#/components/responses/ErrorMessage'
/v1/hubmap/rui_locations.jsonld:
get:
summary: Get all hubmap rui locations (if enabled)
description: This option is only enabled if XCONSORTIA_ROUTES=true in the environment
operationId: hubmap-rui-locations
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
description: Not found due to option being disabled
/v1/sennet/rui_locations.jsonld:
get:
summary: Get all sennet rui locations (if enabled)
description: This option is only enabled if XCONSORTIA_ROUTES=true in the environment
operationId: sennet-rui-locations
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
description: Not found due to option being disabled
/v1/ontology-term-occurences:
get:
summary: Get number of ontology term occurrences for a search
operationId: ontology-term-occurences
tags:
- v1
parameters:
- $ref: '#/components/parameters/Age'
- $ref: '#/components/parameters/AgeRange'
- $ref: '#/components/parameters/Bmi'
- $ref: '#/components/parameters/BmiRange'
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/OntologyTerms'
- $ref: '#/components/parameters/CellTypeTerms'
- $ref: '#/components/parameters/Consortiums'
- $ref: '#/components/parameters/Providers'
- $ref: '#/components/parameters/Sex'
- $ref: '#/components/parameters/SpatialSearches'
- $ref: '#/components/parameters/Technologies'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/TermOccurences'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/cell-type-term-occurences:
get:
summary: Get number of cell type term occurrences for a search
operationId: cell-type-term-occurences
tags:
- v1
parameters:
- $ref: '#/components/parameters/Age'
- $ref: '#/components/parameters/AgeRange'
- $ref: '#/components/parameters/Bmi'
- $ref: '#/components/parameters/BmiRange'
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/OntologyTerms'
- $ref: '#/components/parameters/CellTypeTerms'
- $ref: '#/components/parameters/Consortiums'
- $ref: '#/components/parameters/Providers'
- $ref: '#/components/parameters/Sex'
- $ref: '#/components/parameters/SpatialSearches'
- $ref: '#/components/parameters/Technologies'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/TermOccurences'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/biomarker-term-occurences:
get:
summary: Get number of biomarker type term occurrences for a search
operationId: biomarker-term-occurences
tags:
- v1
parameters:
- $ref: '#/components/parameters/Age'
- $ref: '#/components/parameters/AgeRange'
- $ref: '#/components/parameters/Bmi'
- $ref: '#/components/parameters/BmiRange'
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/OntologyTerms'
- $ref: '#/components/parameters/CellTypeTerms'
- $ref: '#/components/parameters/Consortiums'
- $ref: '#/components/parameters/Providers'
- $ref: '#/components/parameters/Sex'
- $ref: '#/components/parameters/SpatialSearches'
- $ref: '#/components/parameters/Technologies'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/TermOccurences'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/ontology-tree-model:
get:
summary: Get ontology term tree nodes
operationId: ontology-tree-model
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/OntologyTree'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/cell-type-tree-model:
get:
summary: Get cell type tree nodes
operationId: cell-type-tree-model
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/OntologyTree'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/biomarker-tree-model:
get:
summary: Get biomarker tree nodes
operationId: biomarker-tree-model
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/OntologyTree'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/provider-names:
get:
summary: Get tissue provider names (for filtering)
operationId: provider-names
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/Strings'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/reference-organs:
get:
summary: Get all reference organs
operationId: reference-organs
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/SpatialEntities'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/reference-organ-scene:
get:
summary: Get all nodes to form the 3D scene for an organ
operationId: reference-organ-scene
tags:
- v1
parameters:
- $ref: '#/components/parameters/Age'
- $ref: '#/components/parameters/AgeRange'
- $ref: '#/components/parameters/Bmi'
- $ref: '#/components/parameters/BmiRange'
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/OntologyTerms'
- $ref: '#/components/parameters/CellTypeTerms'
- $ref: '#/components/parameters/OrganIri'
- $ref: '#/components/parameters/Consortiums'
- $ref: '#/components/parameters/Providers'
- $ref: '#/components/parameters/Sex'
- $ref: '#/components/parameters/SpatialSearches'
- $ref: '#/components/parameters/Technologies'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/SpatialSceneNodes'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/scene:
get:
summary: Get all nodes to form the 3D scene of reference body, organs, and tissues
operationId: scene
tags:
- v1
parameters:
- $ref: '#/components/parameters/Age'
- $ref: '#/components/parameters/AgeRange'
- $ref: '#/components/parameters/Bmi'
- $ref: '#/components/parameters/BmiRange'
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/OntologyTerms'
- $ref: '#/components/parameters/CellTypeTerms'
- $ref: '#/components/parameters/Consortiums'
- $ref: '#/components/parameters/Providers'
- $ref: '#/components/parameters/Sex'
- $ref: '#/components/parameters/SpatialSearches'
- $ref: '#/components/parameters/Technologies'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/SpatialSceneNodes'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/technology-names:
get:
summary: Get technology names (for filtering)
operationId: technology-names
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/Strings'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/tissue-blocks:
get:
summary: Get Tissue Block Results
operationId: tissue-blocks
tags:
- v1
parameters:
- $ref: '#/components/parameters/Age'
- $ref: '#/components/parameters/AgeRange'
- $ref: '#/components/parameters/Bmi'
- $ref: '#/components/parameters/BmiRange'
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/OntologyTerms'
- $ref: '#/components/parameters/CellTypeTerms'
- $ref: '#/components/parameters/Consortiums'
- $ref: '#/components/parameters/Providers'
- $ref: '#/components/parameters/Sex'
- $ref: '#/components/parameters/SpatialSearches'
- $ref: '#/components/parameters/Technologies'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/TissueBlocks'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/gtex/rui_locations.jsonld:
get:
summary: Get all GTEx rui locations (if enabled)
description: This option is only enabled if GTEX_ROUTES=true in the environment
operationId: gtex-rui-locations
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
description: Not found due to option being disabled
/v1/rui-reference-data:
get:
summary: Get reference data for the RUI tool
operationId: rui-reference-data
tags:
- v1
responses:
'200':
$ref: '#/components/responses/RuiReferenceData'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/anatomical-systems-tree-model:
get:
summary: Get anatomical systems partonomy tree nodes
operationId: anatomical-systems-tree-model
tags:
- v1
parameters:
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/Token'
responses:
'200':
$ref: '#/components/responses/OntologyTree'
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/extraction-site:
get:
summary: Lookup Extraction Site
operationId: extraction-site
tags:
- v1
parameters:
- $ref: '#/components/parameters/ExtractionSiteIri'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/ds-graph:
get:
summary: Get dataset graph
description: Get potentially filtered experimental data in dataset graph format (previously referred to as rui_locations.jsonld format)
operationId: ds-graph
tags:
- v1
parameters:
- $ref: '#/components/parameters/Age'
- $ref: '#/components/parameters/AgeRange'
- $ref: '#/components/parameters/Bmi'
- $ref: '#/components/parameters/BmiRange'
- $ref: '#/components/parameters/Cache'
- $ref: '#/components/parameters/OntologyTerms'
- $ref: '#/components/parameters/CellTypeTerms'
- $ref: '#/components/parameters/Consortiums'
- $ref: '#/components/parameters/Providers'
- $ref: '#/components/parameters/Sex'
- $ref: '#/components/parameters/SpatialSearches'
- $ref: '#/components/parameters/Technologies'
- $ref: '#/components/parameters/Token'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
$ref: '#/components/responses/ErrorMessage'
/v1/collisions:
post:
summary: Given an extraction site, get mesh-based collisions with the reference organ.
operationId: collisions
tags:
- v1
requestBody:
$ref: '#/components/requestBodies/ExtractionSite'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
$ref: '#/components/responses/ErrorMessage'
'500':
$ref: '#/components/responses/ErrorMessage'
/v1/corridor:
post:
summary: Given an extraction site, generate a corridor with the reference organ.
operationId: corridor
tags:
- v1
requestBody:
$ref: '#/components/requestBodies/ExtractionSite'
responses:
'200':
description: Successful operation
content:
model/gltf-binary:
schema:
type: string
format: binary
'404':
$ref: '#/components/responses/ErrorMessage'
'500':
$ref: '#/components/responses/ErrorMessage'
/v1/mesh-3d-cell-population:
post:
summary: Given a reference organ, 3d scene node, and cell population, generate cells in that distribution to fit in that 3d scene node.
operationId: mesh-3d-cell-population
tags:
- v1
requestBody:
$ref: '#/components/requestBodies/Mesh3dCellPopulation'
responses:
'200':
description: Successful response with CSV file
content:
text/csv:
schema:
type: string
format: binary
'404':
$ref: '#/components/responses/ErrorMessage'
'500':
$ref: '#/components/responses/ErrorMessage'
/hra-pop/cell-summary-report:
post:
summary: Given a cell summary in csv format, retrieve a predicted cell summary report from HRApop showing relative anatomical structures, datasets, and rui locations.
operationId: cell-summary-report
tags:
- hra-pop
requestBody:
$ref: '#/components/requestBodies/GetCellSummaryReport'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
$ref: '#/components/responses/ErrorMessage'
'500':
$ref: '#/components/responses/ErrorMessage'
/hra-pop/rui-location-cell-summary:
post:
summary: Given a SpatialEntity already placed relative to a reference SpatialEntity, retrieve a predicted cell summary from HRApop
operationId: rui-location-cell-summary
tags:
- hra-pop
requestBody:
$ref: '#/components/requestBodies/GetRuiLocationCellSummary'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
$ref: '#/components/responses/ErrorMessage'
'500':
$ref: '#/components/responses/ErrorMessage'
/hra-pop/supported-organs:
get:
summary: Get all organs supported by HRApop
operationId: supported-organs
tags:
- hra-pop
responses:
'200':
$ref: '#/components/responses/IdLabelsResponse'
'404':
$ref: '#/components/responses/ErrorMessage'
'500':
$ref: '#/components/responses/ErrorMessage'
/hra-pop/supported-reference-organs:
get:
summary: Get all reference organs supported by HRApop
operationId: supported-reference-organs
tags:
- hra-pop
responses:
'200':
$ref: '#/components/responses/IdLabelsResponse'
'404':
$ref: '#/components/responses/ErrorMessage'
'500':
$ref: '#/components/responses/ErrorMessage'
/hra-pop/supported-tools:
get:
summary: Get all tools supported by HRApop
operationId: supported-tools
tags:
- hra-pop
responses:
'200':
$ref: '#/components/responses/IdLabelsResponse'
'404':
$ref: '#/components/responses/ErrorMessage'
'500':
$ref: '#/components/responses/ErrorMessage'
/ds-graph/hubmap:
get:
summary: Get HuBMAP Dataset Graph
operationId: hubmap
tags:
- ds-graph
parameters:
- $ref: '#/components/parameters/Token'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
$ref: '#/components/responses/ErrorMessage'
/ds-graph/sennet:
get:
summary: Get SenNet Dataset Graph
operationId: sennet
tags:
- ds-graph
parameters:
- $ref: '#/components/parameters/Token'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
$ref: '#/components/responses/ErrorMessage'
/ds-graph/gtex:
get:
summary: Get GTEx Dataset Graph
operationId: gtex
tags:
- ds-graph
parameters:
- $ref: '#/components/parameters/Token'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
$ref: '#/components/responses/ErrorMessage'
/ds-graph/atlas-d2k:
get:
summary: Get Atlas D2K Dataset Graph
operationId: atlas-d2k
tags:
- ds-graph
parameters:
- $ref: '#/components/parameters/Token'
responses:
'200':
description: Successful operation
content:
application/json:
schema:
type: object
'404':
$ref: '#/components/responses/ErrorMessage'
components:
schemas:
MinMaxArray:
title: Number Range
description: |
Represents a range of numbers using a minimum and maximum. First element should be less than or equal to the second element.
type: array
minItems: 2
maxItems: 2
items:
type: number
SpatialSearch:
title: Probing Sphere
description: |
Specification for a Spatial Search via Probing Sphere
type: object
properties:
x:
title: X coordinate relative to target in millimeters
type: number
'y':
title: Y coordinate relative to target in millimeters
type: number
z:
title: Z coordinate relative to target in millimeters
type: number
radius:
title: Size of the probing sphere in millimeters
type: number
target:
title: The target spatial entity IRI
type: string
required:
- x
- 'y'
- z
- radius
- target
additionalProperties: false
Filter:
title: Filter
description: Filter object
type: object
properties:
sex:
type: string
enum:
- Both
- Male
- Female
ageRange:
$ref: '#/components/schemas/MinMaxArray'
bmiRange:
$ref: '#/components/schemas/MinMaxArray'
consortiums:
type: array
items:
type: string
tmc:
type: array
items:
type: string
technologies:
type: array
items:
type: string
ontologyTerms:
type: array
items:
type: string
format: uri
cellTypeTerms:
type: array
items:
type: string
format: uri
biomarkerTerms:
type: array
items:
type: string
format: uri
spatialSearches:
type: array
items:
$ref: '#/components/schemas/SpatialSearch'
additionalProperties: false
SessionTokenRequest:
title: session-token request body
type: object
required:
- dataSources
properties:
dataSources:
type: array
items: {}
filter:
$ref: '#/components/schemas/Filter'
SessionToken:
title: Session Token
type: object
required:
- token
properties:
token:
title: Session token
type: string
ErrorMessage:
title: Error Message
type: object
required:
- error
properties:
error:
title: Human readable description of the error
type: string
DatabaseStatus:
title: Database Status
type: object
required:
- status
properties:
status:
title: Current status of the database
enum:
- Loading
- Ready
- Error
x-preprocessor-delete: enum
checkback:
title: How long to wait (in milliseconds) before checking status again
type: integer
minimum: 0
loadTime:
title: The amount of time (in milliseconds) taken to load the database
type: integer
minimum: 0
message:
title: Human readable description of the current status
type: string
SparqlQueryRequest:
title: SPARQL query request body
type: object
required:
- query
properties:
query:
type: string
MinMax:
title: Number Range
description: |
Represents a range of numbers using a minimum and maximum.
Either end may be omitted to indicate an unlimited/infinite range in that direction.
`min` should be less than or equal to `max` but this is not strictly enforced.
type: object
properties:
min:
type: number
max:
type: number
AggregateCount:
title: Aggregated Count \w Label
type: object
required:
- label
- count
properties:
label:
title: Aggregate Name/Field
type: string
count:
title: Aggregated Count
oneOf:
- type: number
nullable: false
- type: string
nullable: false
x-preprocessor-delete: oneOf
JsonLdObject:
title: JSON-LD Object
description: Base object for all json-ld objects.
type: object
required:
- '@id'
- '@type'
additionalProperties: true
properties:
'@id':
title: Unique Identifier
type: string
format: uri
example: http://purl.obolibrary.org/obo/UBERON_0013702
'@type':
title: Object Type
description: Contains the name of object class/interface
type: string
example: Sample
x-preprocessor-delete:
- properties/@id
- properties/@type
SpatialEntityCommon:
title: Spatial Entity Common
description: Properties available in all spatial entity objects.
type: object
properties:
entityId:
title: Entity Identifier
description: Identifier of the entity the spatial object represents.
type: string
format: uri
ccf_annotations:
title: Annotations
description: Annotations attached to the entity.
type: array
items:
type: string
format: uri
representation_of:
title: Representation
description: Identifier for the item the spatial object represents.
type: string
format: uri
reference_organ:
title: Organ
description: Identifier for the organ the spatial object represents.
type: string
format: uri
sex:
title: Sex
type: string
enum:
- Female
- Male
x-preprocessor-delete: enum
SpatialEntityCreator:
title: Spatial Entity Creator
description: Describes by whom and when an entity object was created.
type: object
properties:
creator:
title: Full Name
type: string
creator_first_name:
title: First Name
type: string
creator_last_name:
title: Last Name
type: string
creator_orcid:
title: Creator's Identifier
type: string
creation_date:
title: Creation Date
type: string
format: date
SpatialEntityDimensions:
title: Spatial Entity Dimensions
description: The dimensions of a spatial entity.
type: object
required:
- x_dimension
- y_dimension
- z_dimension
- dimension_units
properties:
x_dimension:
title: X-Dimension
type: number
y_dimension:
title: Y-Dimension
type: number
z_dimension:
title: Z-Dimension
type: number
dimension_units:
title: Dimension Units
description: Length units of dimensional values.
type: string
default: millimeter
SpatialPlacementTranslation:
title: Spatial Placement Translation
description: The properties to define the Translation aspect of Spatial Placements.
type: object
required:
- x_translation
- y_translation
- z_translation
- translation_units
properties:
x_translation:
title: X-Translation
type: number
y_translation:
title: Y-Translation
type: number
z_translation:
title: Z-Translation
type: number
translation_units:
title: Translation Units
description: Length units of translation values.
type: string