Benchling Enzyme API

openapi: 3.2.0
info:
  title: Benchling Enzyme API
  version: 2.0.0
  license:
    name: Apache 2.0
    url: http://www.apache.org/licenses/LICENSE-2.0.html
  description: 'Operations tagged Enzyme across 2 of this provider''s published API definitions: benchling-openapi.yml, benchling-v3-openapi.yaml. Each path carries the servers of the definition it was published in.'
servers:
- url: /api/v3
security:
- oAuth: []
- basicApiKeyAuth: []
tags:
- 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.'
  name: Enzyme
  x-bnch-organization: Benchling
  x-displayName: Enzyme
paths:
  /enzyme/items:
    get:
      description: List Enzyme items.
      operationId: Enzyme.List
      parameters:
      - $ref: '#/components/parameters/id.anyOf'
      - $ref: '#/components/parameters/name.anyOf'
      - $ref: '#/components/parameters/name.anyOf.caseSensitive'
      - $ref: '#/components/parameters/nextToken'
      - $ref: '#/components/parameters/omit'
      - $ref: '#/components/parameters/pageSize'
      - $ref: '#/components/parameters/returning'
      - 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/EnzymePaginatedList'
          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:
      - Enzyme
    servers:
    - url: /api/v3
  /enzyme/{enzyme_id}:
    get:
      description: Get a single Enzyme by ID.
      operationId: Enzyme.Get
      parameters:
      - description: ID of the Enzyme.
        in: path
        name: enzyme_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/Enzyme'
          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 Enzyme by ID
      tags:
      - Enzyme
    servers:
    - url: /api/v3
  /enzyme/{enzyme_id}/isoschizomers/items:
    get:
      description: List Enzyme items.
      operationId: Enzyme.isoschizomers.List
      parameters:
      - description: ID of the Enzyme.
        in: path
        name: enzyme_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:
      - Enzyme
    servers:
    - url: /api/v3
components:
  schemas:
    EnzymePaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/Enzyme'
          type: array
        nextToken:
          type:
          - string
          - 'null'
      type: object
    EnzymeUnpaginatedList:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/Enzyme'
          type: array
      type: object
    GeneralError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        instance:
          type: string
        invalidId:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      type: object
    TooManyRequestsError:
      properties:
        detail:
          type:
          - 'null'
          - string
          - object
        instance:
          type: string
        invalidId:
          type: string
        status:
          type: integer
        title:
          type:
          - 'null'
          - string
        type:
          type: string
      required:
      - type
      - title
      - detail
      - status
      - instance
      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
    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
    GeneralError_2:
      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
    EnzymePaginatedList_2:
      additionalProperties: false
      properties:
        items:
          items:
            $ref: '#/components/schemas/Enzyme'
          type: array
        nextToken:
          type: string
      type: object
  responses:
    BadRequest:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Bad Request
    NotFound:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Not Found
    Forbidden:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError'
      description: Forbidden
    TooManyRequests:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/TooManyRequestsError'
      description: Too Many Requests
      headers:
        Retry-After:
          description: Minimum number of seconds to wait before retrying. Only included when the request exceeded a rate limit specific to the caller. Limits shared with other callers, such as tenant-wide limits, omit this header because the wait depends on their traffic.
          required: false
          schema:
            minimum: 1
            type: integer
    InternalServerError:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/InternalServerError'
      description: Internal Server Error
    TooManyRequests_2:
      content:
        application/problem+json:
          schema:
            $ref: '#/components/schemas/GeneralError_2'
      description: Too Many Requests
  parameters:
    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
    name.anyOf:
      description: Restricts results to those that match any of the specified names. Case insensitive. Warning - this filter can be non-performant due to case insensitivity. Ensure only one name filter is used at a time. Comma-separated list.
      explode: false
      in: query
      name: name.anyOf
      schema:
        items:
          type: string
        maxItems: 100
        type: array
    nextToken:
      description: Token for pagination
      in: query
      name: nextToken
      schema:
        type: string
    name.anyOf.caseSensitive:
      description: Restricts results to those that match any of the specified names. Case sensitive. Ensure only one name filter is used at a time. Comma-separated list.
      explode: false
      in: query
      name: name.anyOf.caseSensitive
      schema:
        items:
          type: string
        maxItems: 100
        type: array
    pageSize:
      description: Number of results to return. Defaults to 50, maximum of 100.
      in: query
      name: pageSize
      schema:
        type: integer
    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
    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
  securitySchemes:
    BearerAuth:
      description: Use a short-lived V3 API Explorer token.
      scheme: bearer
      type: http
      x-fern-playground-description: Copy a short-lived V3 API Explorer token from the user's settings page
    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
x-refined-from:
- benchling-openapi.yml
- benchling-v3-openapi.yaml