Benchling Enzyme List API

openapi: 3.2.0
info:
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  title: Benchling Enzyme List API
  version: 2.0.0
  description: 'Represents a user-curated collection of restriction enzymes for molecular cloning workflows.

    EnzymeLists allow users and organizations to organize commonly used enzymes into named groups

    for easy access when planning restriction digests, cloning strategies, or analyzing DNA

    sequences. Each list has an owner (either a user or organization) who controls access

    permissions. See `Enzyme` for the individual restriction enzymes that can be added to a list.'
servers:
- url: /api/v3
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- description: 'Represents a user-curated collection of restriction enzymes for molecular cloning workflows.

    EnzymeLists allow users and organizations to organize commonly used enzymes into named groups

    for easy access when planning restriction digests, cloning strategies, or analyzing DNA

    sequences. Each list has an owner (either a user or organization) who controls access

    permissions. See `Enzyme` for the individual restriction enzymes that can be added to a list.'
  name: EnzymeList
  x-bnch-organization: Benchling
paths:
  /enzyme-list/items:
    get:
      description: List EnzymeList items.
      operationId: EnzymeList.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
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/EnzymeListPaginatedList'
          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 EnzymeList items
      tags:
      - EnzymeList
      x-bnch-rate-limit-tier: 4
  /enzyme-list/{enzyme_list_id}:
    get:
      description: Get a single EnzymeList by ID.
      operationId: EnzymeList.Get
      parameters:
      - description: ID of the EnzymeList.
        in: path
        name: enzyme_list_id
        required: true
        schema:
          type: string
      - $ref: '#/components/parameters/returning'
      - $ref: '#/components/parameters/omit'
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/EnzymeList'
          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 EnzymeList by ID
      tags:
      - EnzymeList
      x-bnch-rate-limit-tier: 5
  /enzyme-list/{enzyme_list_id}/enzymes/items:
    get:
      description: List Enzyme items.
      operationId: EnzymeList.enzymes.List
      parameters:
      - description: ID of the EnzymeList.
        in: path
        name: enzyme_list_id
        required: true
        schema:
          type: string
      - description: Set to true to access beta operations via /api/v3.
        in: header
        name: EARLY-ACCESS
        required: false
        schema:
          type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/EnzymeUnpaginatedList'
          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 Enzyme items
      tags:
      - EnzymeList
      x-bnch-rate-limit-tier: 4
components:
  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
  schemas:
    EnzymeListPaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/EnzymeList'
          type: array
        nextToken:
          type: string
      type: object
    OwnerRef:
      properties:
        __typename:
          type: string
        id:
          format: api_id
          type: string
      type: object
    EnzymeList:
      description: 'Represents a user-curated collection of restriction enzymes for molecular cloning workflows.

        EnzymeLists allow users and organizations to organize commonly used enzymes into named groups

        for easy access when planning restriction digests, cloning strategies, or analyzing DNA

        sequences. Each list has an owner (either a user or organization) who controls access

        permissions. See `Enzyme` for the individual restriction enzymes that can be added to a list.'
      properties:
        __typename:
          type: string
        createdAt:
          description: DateTime the Enzyme List was created
          format: datetime
          type: string
        description:
          description: Description of the Enzyme List
          type:
          - 'null'
          - string
        enzymes:
          description: List of Enzymes that are part of this Enzyme List
          format: uri
          type: string
        id:
          description: Id of the Enzyme List
          type: string
        modifiedAt:
          description: DateTime the Enzyme List was last modified
          format: datetime
          type: string
        name:
          description: Name of the Enzyme List
          type: string
        owner:
          $ref: '#/components/schemas/OwnerRef'
          description: User or Organization owner
      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
    EnzymeUnpaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/Enzyme'
          type: array
      type: object
    CutSiteDetail:
      description: 'Describes the cleavage pattern of a restriction enzyme relative to its recognition site.

        The position field indicates where the 5'' strand is cut, while offset specifies the distance

        from position where the 3'' strand is cut. A zero offset produces blunt ends; non-zero offsets

        create sticky ends (overhangs). Enzymes that cut once have a single CutSiteDetail, while

        rare double-cutting enzymes have two. This information is essential for predicting fragment

        sizes and compatible ends when designing cloning strategies.'
      properties:
        __typename:
          type: string
        offset:
          description: Location, relative to `position`, where the 3' cut is made.
          type: integer
        position:
          description: Location, relative to the restriction site bases, where the 5' cut is made.
          type: integer
      type: object
    Enzyme:
      description: 'Represents a restriction enzyme from Benchling''s global catalog of commercially available

        enzymes. Restriction enzymes (also known as restriction endonucleases) are molecular scissors

        that recognize specific DNA sequences and cleave the DNA at defined positions. Each enzyme

        has a recognition sequence (restrictionSiteBases), such as GAATTC for EcoRI, and cut site

        details (see CutSiteDetail) specifying where the enzyme cuts relative to that recognition

        site. Enzymes can produce blunt ends or sticky ends (overhangs) depending on their cut

        pattern. Users can organize frequently used enzymes into EnzymeLists for convenient access

        during cloning workflow design.'
      properties:
        __typename:
          type: string
        cutSites:
          description: Either one (for single cutters) or two (for double cutters) cut details.
          items:
            $ref: '#/components/schemas/CutSiteDetail'
          type: array
        id:
          description: Id of the Enzyme
          type: string
        isoschizomers:
          description: Other enzymes in the catalog that recognize the same restriction site.
          format: uri
          type: string
        name:
          description: The name of the Enzyme, like EcoRI.
          type: string
        restrictionSiteBases:
          description: The DNA bases recognized by the Enzyme.
          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
  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