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Benchling DNA Sequences API

DNA sequences are the bread and butter of the Benchling Molecular Biology suite. On Benchling, these are comprised of a string of nucleotides and collections of other attributes, such as annotations and primers.

Benchling DNA 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 DNA 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 19 operations across 17 paths, and defines 56 schemas. It is described by OpenAPI 3.0.1, at version 2.0.0.

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

19 operations 17 paths 56 schemas 3 GET2 PATCH14 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 DNA 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 19

Across 17 paths, the API surfaces 19 operations — 3 GET, 2 PATCH, 14 POST. Each is listed below with its method, path, parameters, and response codes.

DNA Sequences 19

DNA sequences are the bread and butter of the Benchling Molecular Biology suite. On Benchling, these are comprised of a string of nucleotides and collections of other attributes,…

GET
/dna-sequences
List DNA sequences
listDNASequences 23 params → 200400
POST
/dna-sequences
Create a DNA sequence
createDNASequence body → 201400503
GET
/dna-sequences/{dna_sequence_id}
Get a DNA sequence
getDNASequence 2 params → 200400
PATCH
/dna-sequences/{dna_sequence_id}
Update a DNA sequence
updateDNASequence 1 param body → 200400
PATCH
/dna-sequences/{entity_registry_id}:upsert
Create or update a registered DNA sequence
upsertDNASequence 1 param body → 200201400
POST
/dna-sequences:archive
Archive DNA sequences
archiveDNASequences body → 200400
POST
/dna-sequences:auto-annotate
Auto-annotate DNA sequences with matching features from specified Feature Libraries
autoAnnotateDnaSequences body → 202400
POST
/dna-sequences:autofill-parts
Autofill DNA sequence parts
autofillDNASequenceParts body → 202400
POST
/dna-sequences:autofill-transcriptions
Autofill DNA sequence transcriptions
autofillDNASequenceTranscriptions body → 202400
POST
/dna-sequences:autofill-translations
Autofill DNA sequence translations
autofillDNASequenceTranslations body → 202400
POST
/dna-sequences:bulk-create
Bulk Create DNA sequences
bulkCreateDNASequences body → 202400
GET
/dna-sequences:bulk-get
Bulk get DNA sequences by ID
bulkGetDNASequences 2 params → 200400
POST
/dna-sequences:bulk-update
Bulk Update DNA sequences
bulkUpdateDNASequences body → 202400
POST
/dna-sequences:bulk-upsert
Bulk upsert DNA sequences
bulkUpsertDnaSequences 1 param body → 202400
POST
/dna-sequences:find-matching-regions
Find matching regions for DNA sequences
findMatchingRegionsDnaSequences body → 202400
POST
/dna-sequences:match-bases
List entities with matching bases
matchBasesDnaSequences body → 200400
POST
/dna-sequences:optimize-codons
Create codon-optimized DNA sequences.
optimizeCodons body → 202400
POST
/dna-sequences:search-bases
Search DNA Sequences
searchDnaSequences body → 200400
POST
/dna-sequences:unarchive
Unarchive DNA sequences
unarchiveDNASequences body → 200400

Schemas 56

The contract defines 56 schemas that model the data the API accepts and returns. The most detailed are DnaSequence (27 properties), DnaSequenceBaseRequest (13 properties), OptimizeCodons (11 properties), Primer (9 properties). Each schema is shown below with its type and property counts.

DnaSequencesFindMatchingRegion
object
3 properties 2 required
DnaSequenceUpsertRequest
Primer
object
9 properties
DnaSequencesArchivalChange
object
IDs of all items that were archived or unarchived, grouped by resource type. This includes the IDs of DNA sequences along with any IDs of batches that were arc…
2 properties
Fields
object
DnaSequenceBaseRequestForCreate
FieldWithResolution
SearchBasesRequest
object
7 properties 1 required
DnaSequencesPaginatedList
object
2 properties
DnaSequenceRequestRegistryFields
object
1 property
CustomField
object
1 property
NucleotideSequencePart
object
3 properties
BadRequestError
object
1 property
SequenceFeatureCustomField
object
A name and value pair associated with a sequence feature (annotation or translation). For genbank imports, these are the qualifiers associated with each featur…
2 properties
DnaAnnotation
SequenceFeatureBase
object
4 properties
ArchiveRecordSet
object
Currently, we only support setting a null value for archiveRecord, which unarchives the item
DnaSequenceBaseRequest
object
13 properties
DnaSequenceCreate
SchemaFieldsQueryParam
object
DnaSequencesBulkUpdateRequest
object
1 property
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
OptimizeCodons
object
11 properties 2 required
BaseError
object
3 properties
FieldType
string
FieldsWithResolution
object
FieldValueWithResolution
DnaSequenceUpdate
NamingStrategy
string
Specifies the behavior for automatically generated names when registering an entity. - NEWIDS: Generate new registry IDs - IDSFROMNAMES: Generate registry IDs…
DnaSequencesArchive
object
The request body for archiving DNA sequences.
2 properties 2 required
UserSummary
DnaSequenceBulkUpsertRequest
MatchBasesRequest
object
6 properties 1 required
DnaSequenceBulkUpdate
Translation
Field
object
5 properties 1 required
DnaSequenceTranscription
object
4 properties
DnaSequencePart
PartySummary
object
3 properties
DnaSequenceBulkCreate
DnaSequencesUnarchive
object
The request body for unarchiving DNA sequences.
1 property 1 required
DnaSequencesBulkCreateRequest
object
1 property
AsyncTaskLink
object
1 property
CustomFields
object
EntityBulkUpsertBaseRequest
AutoAnnotateDnaSequences
object
2 properties 2 required
AutofillSequences
object
1 property 1 required
DnaSequencesBulkGet
object
1 property
RegistrationOrigin
object
2 properties
EntityUpsertBaseRequest
object
5 properties 3 required
CreateEntityIntoRegistry
object
4 properties
DnaSequencesBulkUpsertRequest
object
1 property 1 required
DnaSequence
object
27 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-dna-sequences-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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