Benchling Feature Library API

openapi: 3.2.0
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling Feature Library API
  version: 2.0.0
  description: 'Represents a reusable collection of biological features for auto-annotating nucleotide and AA sequences.

    FeatureLibraries enable users to define common sequence motifs (such as genes, promoters, terminators, or

    protein domains) with associated patterns, then automatically detect and annotate those features across many

    sequences. Each library contains `FeatureLibraryItem`s that specify the pattern to match and the annotation

    details to apply. Libraries can be shared with collaborators through ownership and permission controls, making

    them useful for standardizing annotation practices across a team. When running auto-annotate on a sequence,

    users select which libraries to search against.'
servers:
- url: /api/v3
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- description: 'Represents a reusable collection of biological features for auto-annotating nucleotide and AA sequences.

    FeatureLibraries enable users to define common sequence motifs (such as genes, promoters, terminators, or

    protein domains) with associated patterns, then automatically detect and annotate those features across many

    sequences. Each library contains `FeatureLibraryItem`s that specify the pattern to match and the annotation

    details to apply. Libraries can be shared with collaborators through ownership and permission controls, making

    them useful for standardizing annotation practices across a team. When running auto-annotate on a sequence,

    users select which libraries to search against.'
  name: FeatureLibrary
  x-bnch-organization: Benchling
paths:
  /feature-library/items:
    get:
      description: List FeatureLibrary items.
      operationId: FeatureLibrary.List
      parameters:
      - $ref: '#/components/parameters/createdAt.gt'
      - $ref: '#/components/parameters/createdAt.gte'
      - $ref: '#/components/parameters/createdAt.lt'
      - $ref: '#/components/parameters/createdAt.lte'
      - $ref: '#/components/parameters/id.anyOf'
      - $ref: '#/components/parameters/modifiedAt.gt'
      - $ref: '#/components/parameters/modifiedAt.gte'
      - $ref: '#/components/parameters/modifiedAt.lt'
      - $ref: '#/components/parameters/modifiedAt.lte'
      - $ref: '#/components/parameters/nextToken'
      - $ref: '#/components/parameters/omit'
      - $ref: '#/components/parameters/pageSize'
      - $ref: '#/components/parameters/returning'
      - description: 'Method by which to order results. Valid sorts are: createdAt (created time, oldest first) and modifiedAt (modified time, oldest first). Use :asc or :desc to specify ascending or descending order. Default is modifiedAt:desc.'
        in: query
        name: sort
        schema:
          default: modifiedAt:desc
          enum:
          - createdAt:asc
          - createdAt:desc
          - modifiedAt:asc
          - modifiedAt:desc
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FeatureLibraryPaginatedList'
          description: OK
          headers: {}
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: List FeatureLibrary items
      tags:
      - FeatureLibrary
      x-bnch-rate-limit-tier: 4
  /feature-library/{feature_library_id}:
    get:
      description: Get a single FeatureLibrary by ID.
      operationId: FeatureLibrary.Get
      parameters:
      - description: ID of the FeatureLibrary.
        in: path
        name: feature_library_id
        required: true
        schema:
          type: string
      - $ref: '#/components/parameters/returning'
      - $ref: '#/components/parameters/omit'
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FeatureLibrary'
          description: OK
          headers: {}
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: Get FeatureLibrary by ID
      tags:
      - FeatureLibrary
      x-bnch-rate-limit-tier: 5
  /feature-library/{feature_library_id}/features/items:
    get:
      description: List FeatureLibraryItem items.
      operationId: FeatureLibrary.features.List
      parameters:
      - $ref: '#/components/parameters/nextToken'
      - $ref: '#/components/parameters/pageSize'
      - description: ID of the FeatureLibrary.
        in: path
        name: feature_library_id
        required: true
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FeatureLibraryItemPaginatedList'
          description: OK
          headers: {}
        '400':
          $ref: '#/components/responses/BadRequest'
        '403':
          $ref: '#/components/responses/Forbidden'
        '404':
          $ref: '#/components/responses/NotFound'
        '429':
          $ref: '#/components/responses/TooManyRequests'
        '500':
          $ref: '#/components/responses/InternalServerError'
      summary: List FeatureLibraryItem items
      tags:
      - FeatureLibrary
      x-bnch-rate-limit-tier: 4
components:
  schemas:
    FeatureLibraryRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    FeatureLibrary:
      description: 'Represents a reusable collection of biological features for auto-annotating nucleotide and AA sequences.

        FeatureLibraries enable users to define common sequence motifs (such as genes, promoters, terminators, or

        protein domains) with associated patterns, then automatically detect and annotate those features across many

        sequences. Each library contains `FeatureLibraryItem`s that specify the pattern to match and the annotation

        details to apply. Libraries can be shared with collaborators through ownership and permission controls, making

        them useful for standardizing annotation practices across a team. When running auto-annotate on a sequence,

        users select which libraries to search against.'
      properties:
        __typename:
          type: string
        createdAt:
          description: DateTime the Feature Library was created
          format: datetime
          type: string
        description:
          description: Description of the Feature Library
          type:
          - 'null'
          - string
        features:
          description: List of Feature Library Items in this library
          format: uri
          type: string
        id:
          type: string
        modifiedAt:
          description: DateTime the Feature Library was last modified
          format: datetime
          type: string
        name:
          description: Name of the Feature Library
          type: string
        owner:
          $ref: '#/components/schemas/OwnerRef'
      type: object
    FeatureLibraryItemPaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/FeatureLibraryItem'
          type: array
        nextToken:
          type: string
      type: object
    OwnerRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    InternalServerError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        errorId:
          type: string
        instance:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
    FeatureLibraryPaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/FeatureLibrary'
          type: array
        nextToken:
          type: string
      type: object
    FeatureLibraryItem:
      description: 'Represents a single feature definition within a FeatureLibrary used for auto-annotation.

        Each item defines a searchable pattern (nucleotide or amino acid sequence), a feature type

        classification (such as ''gene'', ''promoter'', or ''domain''), a display name, and a color for

        visualization. When auto-annotate runs against a sequence, the pattern is matched according

        to the matchType (see FeatureLibraryMatchType), and matching regions are annotated with the

        item''s name, type, and color. Patterns can include special characters for flexible matching,

        such as wildcards for arbitrary bases or optional flanking regions.'
      properties:
        __typename:
          type: string
        color:
          description: The color of the annotations generated by the Feature Library Item. Must be a valid hex string
          type: string
        createdAt:
          description: DateTime the Feature Library Item was created
          format: datetime
          type: string
        featureLibrary:
          $ref: '#/components/schemas/FeatureLibraryRef'
          description: The Feature Library the Feature Library Item belongs to
        featureType:
          description: 'The type of the Feature Library Item, like gene, promoter, etc. Note: This is an arbitrary string, not an enum'
          type:
          - 'null'
          - string
        id:
          type: string
        matchType:
          description: The match type of the Feature Library Item. Used to determine how auto-annotate matches are made
          enum:
          - NUCLEOTIDE
          - AA_SEQUENCE
          type: string
        modifiedAt:
          description: DateTime the Feature Library Item was last modified
          format: datetime
          type: string
        name:
          description: The name of the Feature Library Item
          type: string
        pattern:
          description: The pattern used for matching during auto-annotation
          type: string
      type: object
    GeneralError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        instance:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
  parameters:
    pageSize:
      description: Number of results to return. Defaults to 50, maximum of 100.
      in: query
      name: pageSize
      schema:
        type: integer
    createdAt.gte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created at or after the specified time. e.g. >= 2017-04-30.
      in: query
      name: createdAt.gte
      schema:
        format: datetime
        type: string
    modifiedAt.gt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified after the specified time. e.g. > 2017-04-30.
      in: query
      name: modifiedAt.gt
      schema:
        format: datetime
        type: string
    modifiedAt.lte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified at or before the specified time. e.g. <= 2017-04-30.
      in: query
      name: modifiedAt.lte
      schema:
        format: datetime
        type: string
    id.anyOf:
      description: Restricts results to those matching any of the specified IDs. Comma-separated list.
      explode: false
      in: query
      name: id.anyOf
      schema:
        items:
          type: string
        maxItems: 100
        type: array
    omit:
      description: Comma-separated list of top-level fields to omit from each returned item. Cannot overlap with returning.
      explode: false
      in: query
      name: omit
      schema:
        items:
          type: string
        type: array
    modifiedAt.lt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified before the specified time. e.g. < 2017-04-30.
      in: query
      name: modifiedAt.lt
      schema:
        format: datetime
        type: string
    createdAt.gt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created after the specified time. e.g. > 2017-04-30.
      in: query
      name: createdAt.gt
      schema:
        format: datetime
        type: string
    createdAt.lt:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created before the specified time. e.g. < 2017-04-30.
      in: query
      name: createdAt.lt
      schema:
        format: datetime
        type: string
    returning:
      description: Comma-separated list of top-level fields to include in each returned item. Cannot overlap with omit.
      explode: false
      in: query
      name: returning
      schema:
        items:
          type: string
        type: array
    nextToken:
      description: Token for pagination
      in: query
      name: nextToken
      schema:
        type: string
    modifiedAt.gte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those modified at or after the specified time. e.g. >= 2017-04-30.
      in: query
      name: modifiedAt.gte
      schema:
        format: datetime
        type: string
    createdAt.lte:
      description: Datetime, in RFC 3339 format. Time zone defaults to UTC. Restricts results to those created at or before the specified time. e.g. <= 2017-04-30.
      in: query
      name: createdAt.lte
      schema:
        format: datetime
        type: string
  responses:
    NotFound:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Not Found
    TooManyRequests:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Too Many Requests
    BadRequest:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Bad Request
    Forbidden:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Forbidden
    InternalServerError:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/InternalServerError'
      description: Internal Server Error
  securitySchemes:
    basicApiKeyAuth:
      description: Use issued API key for standard access to the API
      scheme: basic
      type: http
    basicClientIdSecretAuth:
      description: Auth used as part of client credentials OAuth flow prior to receiving a bearer token.
      scheme: basic
      type: http
    oAuth:
      description: OAuth2 Client Credentials flow intended for service access
      flows:
        clientCredentials:
          scopes: {}
          tokenUrl: /oauth/token
      type: oauth2