hra-api/hra-api-spec.yaml

The Human Reference Atlas (HRA) API deployed to https://apps.humanatlas.io/api/

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: 0.15.0
  contact:
    name: HuBMAP Help Desk
    email: help@hubmapconsortium.org
  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-kg
    description: HRA KG Routes
  - name: hra-pop
    description: HRApop Routes
externalDocs:
  description: API Documentation
  url: https://github.com/x-atlas-consortia/hra-api#readme
paths:
  /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/BiomarkerTerms'
        - $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/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/asctb-omap-sheet-config:
    get:
      summary: Get OMAP sheet config data for the ASCT+B Reporter
      operationId: asctb-omap-sheet-config
      tags:
        - v1
      responses:
        '200':
          $ref: '#/components/responses/AsctbReferenceData'
        '404':
          $ref: '#/components/responses/ErrorMessage'
  /v1/asctb-sheet-config:
    get:
      summary: Get sheet config data for the ASCT+B Reporter
      operationId: asctb-sheet-config
      tags:
        - v1
      responses:
        '200':
          $ref: '#/components/responses/AsctbReferenceData'
        '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/BiomarkerTerms'
        - $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-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/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/BiomarkerTerms'
        - $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-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/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/consortium-names:
    get:
      summary: Get consortium names (for filtering)
      operationId: consortium-names
      tags:
        - v1
      parameters:
        - $ref: '#/components/parameters/Cache'
        - $ref: '#/components/parameters/Token'
      responses:
        '200':
          $ref: '#/components/responses/Strings'
        '404':
          $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/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/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/BiomarkerTerms'
        - $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/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/ftu-illustrations:
    get:
      summary: Get 2D FTU Illustration data
      operationId: ftu-illustrations
      tags:
        - v1
      responses:
        '200':
          $ref: '#/components/responses/FtuIllustrations'
        '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/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/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/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'
  /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/BiomarkerTerms'
        - $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/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-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/BiomarkerTerms'
        - $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/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/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/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/BiomarkerTerms'
        - $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/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/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/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/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/BiomarkerTerms'
        - $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'
  /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'
  /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/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'
  /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':
          $ref: '#/components/responses/CellSummaryReportResponse'
        '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':
          $ref: '#/components/responses/RuiLocationCellSummaryResponse'
        '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'
  /kg/asctb-term-occurences:
    get:
      summary: Get number of ASCT+B term occurrences for a search
      operationId: asctb-term-occurences
      tags:
        - hra-kg
      parameters:
        - $ref: '#/components/parameters/OntologyTerms'
        - $ref: '#/components/parameters/CellTypeTerms'
        - $ref: '#/components/parameters/BiomarkerTerms'
      responses:
        '200':
          $ref: '#/components/responses/TermOccurences'
        '404':
          $ref: '#/components/responses/ErrorMessage'
  /kg/digital-objects:
    get:
      summary: List all digital objects in the HRA KG
      operationId: digital-objects
      tags:
        - hra-kg
      responses:
        '200':
          $ref: '#/components/responses/DigitalObjectsResponse'
        '404':
          $ref: '#/components/responses/ErrorMessage'
        '500':
          $ref: '#/components/responses/ErrorMessage'
  /kg/do-search:
    get:
      summary: Search for Digital Object PURLs
      operationId: do-search
      tags:
        - hra-kg
      parameters:
        - $ref: '#/components/parameters/OntologyTerms'
        - $ref: '#/components/parameters/CellTypeTerms'
        - $ref: '#/components/parameters/BiomarkerTerms'
        - $ref: '#/components/parameters/HraVersions'
      responses:
        '200':
          $ref: '#/components/responses/Strings'
        '404':
          $ref: '#/components/responses/ErrorMessage'
        '500':
          $ref: '#/components/responses/ErrorMessage'
components:
  schemas:
    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
    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
    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
    ErrorMessage:
      title: Error Message
      type: object
      required:
        - error
      properties:
        error:
          title: Human readable description of the error
          type: string
    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
    OntologyTreeNode:
      title: Ontology Node
      description: A node in the ontology tree.
      type: object
      allOf:
        - $ref: '#/components/schemas/JsonLdObject'
      required:
        - '@type'
      properties:
        '@type':
          type: string
          enum:
            - OntologyTreeNode
        id:
          title: Identifier
          description: Unique identifier for the node.
          type: string
          format: uri
        label:
          title: Label
          description: Main descriptive label for the node.
          type: string
        synonymLabels:
          title: Synonym Labels
          description: Additional label for the node.
          type: array
          items:
            type: string
        parent:
          title: Parent Node Identifier
          description: Reference to the parent node.
          type: string
          format: uri
        children:
          title: Child Node Identifiers
          description: References to all child nodes.
          type: array
          items:
            type: string
            format: uri
      x-preprocessor-delete:
        - properties/@type
    OntologyTree:
      title: Ontology Tree
      description: An ontology tree.
      type: object
      required:
        - root
        - nodes
      properties:
        root:
          title: Root Node
          description: Reference to the root node.
          type: string
          format: url
        nodes:
          title: All Nodes
          description: A mapping of identifiers to each node object.
          additionalProperties:
            $ref: '#/components/schemas/OntologyTreeNode'
    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
          default: millimeter
          enum:
            - millimeter
          x-preprocessor-delete: enum
    SpatialPlacementRotation:
      title: Spatial Placement Rotation
      description: The properties to define the Rotation aspect of Spatial Placements.
      type: object
      required:
        - x_rotation
        - y_rotation
        - z_rotation
        - rotation_units
      properties:
        x_rotation:
          title: X-Rotation
          type: number
        y_rotation:
          title: Y-Rotation
          type: number
        z_rotation:
          title: Z-Rotation
          type: number
        rotation_units:
          title: Rotation Units
          description: Units of rotation values.
          type: string
          default: degree
          enum:
            - degree
          x-preprocessor-delete: enum
    SpatialPlacementScaling:
      title: Spatial Placement Scaling
      description: The properties to define the Scaling aspect of Spatial Placements.
      type: object
      required:
        - x_scaling
        - y_scaling
        - z_rotation
        - scaling_units
      properties:
        x_scaling:
          title: X-Scaling
          type: number
        y_scaling:
          title: Y-Scaling
          type: number
        z_scaling:
          title: Z-Scaling
          type: number
        scaling_units:
          title: Scaling Units
          description: Units of scaling values.
          type: string
          default: ratio
          enum:
            - ratio
          x-preprocessor-delete: enum
    SpatialPlacementCommon:
      title: Spatial Placement common fields
      description: A Spatial Placement defines how to place a Spatial Entity or Spatial Object Reference relative to another Spatial Entity. It says how to scale, rotate, and translate (in that order) a Spatial Entity or Spatial Object Reference so that it is placed relative to another Spatial Entity.
      type: object
      allOf:
        - $ref: '#/components/schemas/JsonLdObject'
        - $ref: '#/components/schemas/SpatialPlacementTranslation'
        - $ref: '#/components/schemas/SpatialPlacementRotation'
        - $ref: '#/components/schemas/SpatialPlacementScaling'
      required:
        - '@type'
        - target
      properties:
        '@type':
          type: string
          enum:
            - SpatialPlacement
        placement_date:
          title: Date placement was made
          type: string
          format: date
      x-preprocessor-delete:
        - properties/@type
    SpatialEntity:
      title: Spatial Entity
      description: A Spatial Entity defines a bounded cartesian space and the units it is measured in. It typically represents a real world thing, e.g., a human body, a human kidney, a tissue section, or an individual cell.
      type: object
      allOf:
        - $ref: '#/components/schemas/JsonLdObject'
        - $ref: '#/components/schemas/SpatialEntityCommon'
        - $ref: '#/components/schemas/SpatialEntityCreator'
        - $ref: '#/components/schemas/SpatialEntityDimensions'
      required:
        - '@type'
      properties:
        '@type':
          type: string
          enum:
            - SpatialEntity
        label:
          title: Label
          type: string
        comment:
          title: Comment
          type: string
        rui_rank:
          title: RUI Rank
          description: Ranking used to order lists in the RUI.
          type: integer
        sex:
          title: Sex
          type: string
          enum:
            - Female
            - Male
          x-preprocessor-delete: enum
        side:
          title: Side
          description: Used for organs that come in pairs to distinguish between them, i.e. kidneys, etc.
          type: string
          enum:
            - Left
            - Right
          x-preprocessor-delete: enum
        slice_count:
          title: Slice Count
          type: integer
        slice_thickness:
          title: Slice Thickness
          type: number
        placement:
          oneOf:
            - $ref: '#/components/schemas/SpatialPlacement'
            - type: array
              items:
                $ref: '#/components/schemas/SpatialPlacement'
          x-preprocessor-delete: oneOf
        object:
          $ref: '#/components/schemas/SpatialObjectReference'
        color:
          $ref: '#/components/schemas/Rgba'
      x-preprocessor-delete:
        - properties/@type
    SpatialObjectReference:
      title: Spatial Object Reference
      description: A Spatial Object Reference provides a reference to an external representation of a Spatial Entity.
      type: object
      allOf:
        - $ref: '#/components/schemas/JsonLdObject'
      required:
        - '@type'
      properties:
        '@type':
          type: string
          enum:
            - SpatialObjectReference
        file:
          title: File
          type: string
          format: uri
        file_format:
          title: File Format
          type: string
          example: model/gltf-binary
        file_subpath:
          title: File Subpath
          type: string
      x-preprocessor-delete:
        - properties/@type
    SpatialPlacement:
      title: Spatial Placement
      description: A Spatial Placement defines how to place a Spatial Entity or Spatial Object Reference relative to another Spatial Entity. It says how to scale, rotate, and translate (in that order) a Spatial Entity or Spatial Object Reference so that it is placed relative to another Spatial Entity.
      type: object
      allOf:
        - $ref: '#/components/schemas/SpatialPlacementCommon'
      properties:
        source:
          oneOf:
            - $ref: '#/components/schemas/SpatialEntity'
            - $ref: '#/components/schemas/SpatialObjectReference'
          x-preprocessor-delete: oneOf
        target:
          oneOf:
            - title: Target Sptial Entity IRI
              type: string
              format: uri
              example: http://purl.org/ccf/latest/ccf.owl#VHMLeftKidney
            - $ref: '#/components/schemas/SpatialEntity'
          x-preprocessor-delete: oneOf
    Rgba:
      title: RGBA Color Tuple
      type: array
      minItems: 4
      maxItems: 4
      items:
        title: 8-Bit Value
        type: number
        minimum: 0
        maximum: 255
    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
    GetSpatialPlacementRequest:
      title: get-spatial-placement request body
      type: object
      required:
        - target_iri
        - rui_location
      properties:
        target_iri:
          type: string
          format: uri
        rui_location:
          $ref: '#/components/schemas/SpatialEntity'
    FlatSpatialPlacement:
      title: Spatial Placement
      description: A Spatial Placement defines how to place a Spatial Entity or Spatial Object Reference relative to another Spatial Entity. It says how to scale, rotate, and translate (in that order) a Spatial Entity or Spatial Object Reference so that it is placed relative to another Spatial Entity.
      type: object
      allOf:
        - $ref: '#/components/schemas/SpatialPlacementCommon'
      properties:
        source:
          title: Source Spatial Entity or Spatial Object Reference IRI
          type: string
          format: uri
        target:
          title: Target Spatial Entity IRI
          type: string
          format: uri
    Mesh3dCellPopulationRequest:
      title: mesh-3d-cell-population request body
      type: object
      required:
        - file
        - file_subpath
        - num_nodes
        - node_distribution
      properties:
        file:
          type: string
          format: uri
        file_subpath:
          type: string
        num_nodes:
          type: integer
        node_distribution:
          type: object
          additionalProperties:
            type: number
    SpatialSceneNode:
      title: Spatial Scene Node
      description: ''
      type: object
      allOf:
        - $ref: '#/components/schemas/JsonLdObject'
        - $ref: '#/components/schemas/SpatialEntityCommon'
      properties:
        name:
          title: Label
          type: string
        tooltip:
          title: Tooltip Label
          type: string
        unpickable:
          title: Unpickable
          description: Whether the node should selectable by the user in interfaces.
          type: boolean
        geometry:
          title: Geometry
          description: Geometry to draw, if it is not using a GLTF file.
          type: string
          enum:
            - sphere
            - cube
            - wireframe
            - text
            - cone
            - cylinder
          x-preprocessor-delete: enum
        _lighting:
          title: Lighting
          type: string
        zoomBasedOpacity:
          title: Zoom Based Opacity
          description: Whether the opacity of the node changes based on the zoom level.
          type: boolean
        zoomToOnLoad:
          title: Focus
          description: Focus this node when loaded in an interface.
          type: boolean
        scenegraph:
          title: Scenegraph
          type: string
          format: uri
        scenegraphNode:
          title: Scenegraph Node
          type: string
        color:
          $ref: '#/components/schemas/Rgba'
        opacity:
          title: Opacity
          type: number
        transformMatrix:
          title: Transformation
          description: Additional transformations to be applied.
          type: array
          minItems: 16
          maxItems: 16
          items:
            type: number
        priority:
          title: Priority
          type: number
    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
    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
    SparqlQueryRequest:
      title: SPARQL query request body
      type: object
      required:
        - query
      properties:
        query:
          type: string
    TissueCommon:
      title: Common Tissue Data Properties
      description: Properties available in all tissue data objects.
      type: object
      required:
        - label
        - link
      properties:
        label:
          type: string
        description:
          type: string
        link:
          title: Associated URL
          type: string
          format: uri
    TissueDataset:
      title: Tissue Dataset
      description: Describes a single tissue dataset.
      type: object
      allOf:
        - $ref: '#/components/schemas/JsonLdObject'
        - $ref: '#/components/schemas/TissueCommon'
      required:
        - '@type'
      properties:
        '@type':
          type: string
          enum:
            - Dataset
        technology:
          title: Technology Used
          type: string
        thumbnail:
          title: Representative Thumbnail URL
          type: string
          format: uri
      x-preprocessor-delete:
        - properties/@type
    TissueSampleCommon:
      title: Common Tissue Sample Properties
      description: Properties available in all tissue sample objects.
      type: object
      required:
        - '@type'
        - sampleType
        - datasets
      properties:
        '@type':
          type: string
          enum:
            - Sample
        sampleType:
          title: Object Type
          type: string
        datasets:
          title: Associated Datasets
          type: array
          items:
            $ref: '#/components/schemas/TissueDataset'
      x-preprocessor-delete:
        - properties/@type
    TissueDonor:
      title: Tissue Donor
      description: Contains generic information about a tissue donor.
      type: object
      allOf:
        - $ref: '#/components/schemas/JsonLdObject'
        - $ref: '#/components/schemas/TissueCommon'
      required:
        - '@type'
      properties:
        '@type':
          type: string
          enum:
            - Donor
        providerName:
          title: Provider of Donor
          type: string
      x-preprocessor-delete:
        - properties/@type
    TissueSection:
      title: Tissue Section
      description: A single section sample.
      type: object
      allOf:
        - $ref: '#/components/schemas/JsonLdObject'
        - $ref: '#/components/schemas/TissueCommon'
        - $ref: '#/components/schemas/TissueSampleCommon'
      required:
        - sampleType
      properties:
        sampleType:
          type: string
          enum:
            - Tissue Section
            - Non-Standard
          x-preprocessor-delete: enum
        sectionNumber:
          title: Section Index
          description: Index of the section in the parent block.
          type: integer
          minimum: 0
    TissueBlock:
      title: Tissue Block
      description: Information about a collection of tissue sections.
      type: object
      allOf:
        - $ref: '#/components/schemas/JsonLdObject'
        - $ref: '#/components/schemas/TissueCommon'
        - $ref: '#/components/schemas/TissueSampleCommon'
      required:
        - sampleType
      properties:
        sampleType:
          type: string
          enum:
            - Tissue Block
            - Non-Standard
          x-preprocessor-delete: enum
        spatialEntityId:
          title: Associated Spatial Entity
          description: The associated spatial entity (rui_location) for the block.
          type: string
          format: uri
        donor:
          $ref: '#/components/schemas/TissueDonor'
        sectionCount:
          title: Number of Sections
          description: Number of sections contained in the block.
          type: integer
          minimum: 0
        sectionSize:
          title: Section Size
          description: Size of each section in the block.
          type: number
          minimum: 0
        sectionUnits:
          title: Section Size Unit
          description: Length unit `sectionSize` is in (generally, millimeters)
          type: string
          default: millimeter
        sections:
          title: Contained Sections
          description: All sections in the block.
          type: array
          items: