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Benchling AA Sequences API

AA Sequences are the working units of cells that make everything run (they help make structures, catalyze reactions and allow for signaling - a kind of internal cell communication). On Benchling, these are comprised of a string of amino acids and collections of other attributes, such as annotations.

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

Tagged areas include AA Sequences. 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 16 operations across 14 paths, and defines 48 schemas. It is described by OpenAPI 3.0.1, at version 2.0.0.

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

16 operations 14 paths 48 schemas 3 GET2 PATCH11 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 AA Sequences 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 16

Across 14 paths, the API surfaces 16 operations — 3 GET, 2 PATCH, 11 POST. Each is listed below with its method, path, parameters, and response codes.

AA Sequences 16

AA Sequences are the working units of cells that make everything run (they help make structures, catalyze reactions and allow for signaling - a kind of internal cell communication…

GET
/aa-sequences
List AA sequences
listAASequences 23 params → 200400
POST
/aa-sequences
Create an AA sequence
createAASequence body → 201400503
GET
/aa-sequences/{aa_sequence_id}
Get an AA sequence
getAASequence 2 params → 200400
PATCH
/aa-sequences/{aa_sequence_id}
Update an AA sequence
updateAASequence 1 param body → 200400
PATCH
/aa-sequences/{entity_registry_id}:upsert
Create or update a registered AA sequence.
upsertAaSequence 1 param body → 200201400
POST
/aa-sequences:archive
Archive AA sequences
archiveAASequences body → 200400
POST
/aa-sequences:auto-annotate
Auto-annotate AA sequences with matching features from specified Feature Libraries
autoAnnotateAaSequences body → 202400
POST
/aa-sequences:back-translate
Create back-translated DNA sequences from AA sequences.
backTranslate body → 202400
POST
/aa-sequences:bulk-create
Bulk Create AA sequences
bulkCreateAASequences body → 202400
GET
/aa-sequences:bulk-get
Bulk get AA sequences by ID
bulkGetAASequences 2 params → 200400
POST
/aa-sequences:bulk-update
Bulk Update AA sequences
bulkUpdateAASequences body → 202400
POST
/aa-sequences:bulk-upsert
Bulk upsert AA sequences
bulkUpsertAASequences 1 param body → 202400
POST
/aa-sequences:find-matching-regions
Find matching regions for AA sequences
findMatchingRegionsAaSequences body → 202400
POST
/aa-sequences:match-amino-acids
List entities with matching amino acids
matchAminoAcidsAaSequences body → 200400
POST
/aa-sequences:search-amino-acids
Search AA Sequences
searchAaSequences body → 200400
POST
/aa-sequences:unarchive
Unarchive AA sequences
unarchiveAASequences body → 200400

Schemas 48

The contract defines 48 schemas that model the data the API accepts and returns. The most detailed are AaSequence (21 properties), BackTranslate (11 properties), AaSequenceBaseRequest (9 properties), AaAnnotation (7 properties). Each schema is shown below with its type and property counts.

AaSequenceBaseRequestForCreate
AaSequenceBaseRequest
object
9 properties
AaSequenceCreate
AaSequencesBulkUpsertRequest
object
1 property 1 required
Fields
object
FieldWithResolution
CustomField
object
1 property
AaSequenceBulkUpsertRequest
BadRequestError
object
1 property
AaSequenceUpsert
AaSequencesPaginatedList
object
2 properties
AaAnnotation
object
7 properties
SchemaFieldsQueryParam
object
ArchiveRecordSet
object
Currently, we only support setting a null value for archiveRecord, which unarchives the item
BaseError
object
3 properties
ReducedPattern
object
DNA patterns to avoid during optimization. Supports two formats: 1) DNA base patterns: strings of ATGC bases (case-insensitive, e.g., "ATGC" or "gat") 2) Repea…
2 properties
ArchiveRecord
object
1 property
AaSequenceRequestRegistryFields
object
1 property
AaSequencesBulkUpdateRequest
object
1 property
FieldType
string
FieldsWithResolution
object
BackTranslate
object
11 properties 2 required
FieldValueWithResolution
NamingStrategy
string
Specifies the behavior for automatically generated names when registering an entity. - NEWIDS: Generate new registry IDs - IDSFROMNAMES: Generate registry IDs…
UserSummary
AaSequencesMatchBases
object
6 properties 1 required
AaSequenceBulkCreate
Field
object
5 properties 1 required
PartySummary
object
3 properties
AaSequencesBulkGet
object
1 property
AaSequencesSearchBases
object
6 properties 1 required
AaSequencesBulkCreateRequest
object
1 property
AaSequencesArchivalChange
object
IDs of all items that were archived or unarchived, grouped by resource type. This includes the IDs of AA sequences along with any IDs of batches that were arch…
2 properties
AsyncTaskLink
object
1 property
AaSequenceBulkUpdate
CustomFields
object
AaSequenceUpdate
EntityBulkUpsertBaseRequest
AaSequencesArchive
object
The request body for archiving AA sequences.
2 properties 2 required
AaSequencesFindMatchingRegion
object
3 properties 2 required
RegistrationOrigin
object
2 properties
CreateEntityIntoRegistry
object
4 properties
EntityUpsertBaseRequest
object
5 properties 3 required
AaSequencesUnarchive
object
The request body for unarchiving AA sequences.
1 property 1 required
AutoAnnotateAaSequences
object
2 properties 2 required
AaSequence
object
21 properties
SchemaSummary
object
2 properties
EntityArchiveReason
string
The reason for archiving the provided entities. Accepted reasons may differ based on tenant configuration.

Specification

The full machine-readable OpenAPI contract behind this narrative.

Source

benchling-aa-sequences-api-openapi.yml Raw ↑

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