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Benchling Molecules API

Molecules are groups of atoms held together by bonds, representing entities smaller than DNA Sequences and AA Sequences. Just like other entities, they support schemas, tags, and aliases.

Benchling Molecules API is one of 58 APIs that Benchling publishes on the APIs.io network, described by a machine-readable OpenAPI specification.

Tagged areas include Molecules. The published artifact set on APIs.io includes an OpenAPI specification, API documentation, an API reference, authentication docs, a changelog, and a status page.

This API exposes 10 operations across 8 paths, and defines 39 schemas. It is described by OpenAPI 3.0.1, at version 2.0.0.

Requests are made against a single base URL, /api/v2.

10 operations 8 paths 39 schemas 2 GET2 PATCH6 POST

Metadata

The identity and technical contract details declared by the specification.

Specification
OpenAPI 3.0.1
API Version
2.0.0
Base URL
https://{tenant}.benchling.com/api/v2
Authentication
HTTP Basic, HTTP Basic, OAuth 2.0
License
Resource Areas
1

Authentication & Security 3

Benchling Molecules API declares 3 security schemes for authenticating requests. It accepts HTTP basic authentication (basicApiKeyAuth). It accepts HTTP basic authentication (basicClientIdSecretAuth). It supports OAuth 2.0 (oAuth) using the clientCredentials flow. By default, every request must be authenticated.

  • basicApiKeyAuth — Use issued API key for standard access to the API
  • basicClientIdSecretAuth — Auth used as part of client credentials OAuth flow prior to receiving a bearer token.
  • oAuth — OAuth2 Client Credentials flow intended for service access

Paths & Operations 10

Across 8 paths, the API surfaces 10 operations — 2 GET, 2 PATCH, 6 POST. Each is listed below with its method, path, parameters, and response codes.

Molecules 10

Molecules are groups of atoms held together by bonds, representing entities smaller than DNA Sequences and AA Sequences. Just like other entities, they support schemas, tags, and…

GET
/molecules
List Molecules
listMolecules 21 params → 200400
POST
/molecules
Create a Molecule
createMolecule body → 201400503
PATCH
/molecules/{entity_registry_id}:upsert
Create or update a registered Molecule
upsertMolecule 1 param body → 200201400
GET
/molecules/{molecule_id}
Get a Molecule
getMolecule 1 param → 200400
PATCH
/molecules/{molecule_id}
Update a Molecule
updateMolecule 1 param body → 200400
POST
/molecules:archive
Archive Molecules
archiveMolecules body → 200400
POST
/molecules:bulk-create
Bulk Create Molecules
bulkCreateMolecules body → 202400
POST
/molecules:bulk-update
Bulk Update Molecules
bulkUpdateMolecules body → 202400
POST
/molecules:bulk-upsert
Bulk upsert Molecules
bulkUpsertMolecules 1 param body → 202400
POST
/molecules:unarchive
Unarchive Molecules
unarchiveMolecules body → 200400

Schemas 39

The contract defines 39 schemas that model the data the API accepts and returns. The most detailed are Molecule (19 properties), MoleculeBaseRequest (8 properties), EntityUpsertBaseRequest (5 properties), Field (5 properties). Each schema is shown below with its type and property counts.

Molecule
object
19 properties
MoleculeBaseRequestForCreate
MoleculeUpdate
MoleculesPaginatedList
Fields
object
MoleculesArchive
object
The request body for archiving Molecules.
2 properties 2 required
FieldWithResolution
MoleculesArchivalChange
object
IDs of all items that were archived or unarchived, grouped by resource type. This includes the IDs of Molecules along with any IDs of batches that were archive…
2 properties
CustomField
object
1 property
MoleculesBulkUpdateRequest
object
1 property
BadRequestError
object
1 property
ArchiveRecordSet
object
Currently, we only support setting a null value for archiveRecord, which unarchives the item
MoleculesBulkCreateRequest
object
1 property
SchemaFieldsQueryParam
object
BaseError
object
3 properties
Pagination
object
1 property
ArchiveRecord
object
1 property
MoleculeStructure
object
2 properties
MoleculesUnarchive
object
The request body for unarchiving Molecules.
1 property 1 required
FieldType
string
MoleculeBulkUpdate
FieldsWithResolution
object
FieldValueWithResolution
MoleculeBulkUpsertRequest
NamingStrategy
string
Specifies the behavior for automatically generated names when registering an entity. - NEWIDS: Generate new registry IDs - IDSFROMNAMES: Generate registry IDs…
UserSummary
Field
object
5 properties 1 required
PartySummary
object
3 properties
MoleculeCreate
MoleculesBulkUpsertRequest
object
1 property 1 required
AsyncTaskLink
object
1 property
EntityBulkUpsertBaseRequest
CustomFields
object
MoleculeBaseRequest
object
8 properties
MoleculeUpsertRequest
RegistrationOrigin
object
2 properties
EntityUpsertBaseRequest
object
5 properties 3 required
CreateEntityIntoRegistry
object
4 properties
SchemaSummary
object
2 properties

Specification

The full machine-readable OpenAPI contract behind this narrative.

Source

benchling-molecules-api-openapi.yml Raw ↑

Other APIs Benchling publishes across the network.

Benchling AA Sequences API
Benchling Apps API
Benchling Assay Results API
Benchling Assay Runs API
Benchling Audit API
Benchling Authentication API
Benchling Blobs API
Benchling Boxes API
Benchling Codon Usage Tables API
Benchling Connect API
Benchling Containers API
Benchling Custom Entities API
Where this information came from

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