openapi: 3.0.1 info: license: name: Apache 2.0 url: http://www.apache.org/licenses/LICENSE-2.0.html title: Benchling AA Sequences Registry API version: 2.0.0 description: '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. ' servers: - url: /api/v2 security: - oAuth: [] - basicApiKeyAuth: [] tags: - description: 'Manage registry objects. See our documentation on [how to register entities](https://docs.benchling.com/docs/registering-entities). ' name: Registry paths: /registries: get: description: List registries operationId: listRegistries parameters: - description: Name of a registry. Restricts results to those with the specified name. in: query name: name schema: type: string - description: 'Datetime, in RFC 3339 format. Supports the > and < operators. Time zone defaults to UTC. Restricts results to those modified in the specified range. e.g. > 2017-04-30. Date ranges can be specified with the following nomenclature > YYYY-MM-DD AND 2022-03-01 AND < 2022-04-01' full-rfc-3339-format: summary: Filter for modified models using the full RFC 3339 format value: '> 2020-12-31T21:07:14-05:00' greater-than-example: summary: Filter for all models modified after a certain date value: '> 2022-03-01' in: query name: modifiedAt schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/RegistriesList' description: OK summary: List registries tags: - Registry /registries/{registry_id}: get: description: Get registry operationId: getRegistry parameters: - description: ID for the registry in: path name: registry_id required: true schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/Registry' description: OK '404': content: application/json: schema: $ref: '#/components/schemas/NotFoundError' description: Not Found summary: Get registry tags: - Registry /registries/{registry_id}/batch-schemas: get: deprecated: true description: List batch schemas by registry. Deprecated - use Schemas endpoints instead. operationId: listBatchSchemasByRegistry parameters: - description: ID for the registry in: path name: registry_id required: true schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/BatchSchemasList' description: OK '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request summary: List batch schemas by registry tags: - Registry /registries/{registry_id}/box-schemas: get: deprecated: true description: List box schemas by registry. Deprecated - use Schemas endpoints instead. operationId: listBoxSchemasByRegistry parameters: - description: ID for the registry in: path name: registry_id required: true schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/BoxSchemasList' description: OK '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request summary: List box schemas by registry tags: - Registry /registries/{registry_id}/container-schemas: get: deprecated: true description: List container schemas by registry. Deprecated - use Schemas endpoints instead. operationId: listContainerSchemasByRegistry parameters: - description: ID for the registry in: path name: registry_id required: true schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/ContainerSchemasList' description: OK '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request summary: List container schemas by registry tags: - Registry /registries/{registry_id}/dropdowns: get: deprecated: true description: List dropdowns by registry operationId: listDropdownsByRegistry parameters: - description: ID of the registry to list the dropdowns for. in: path name: registry_id required: true schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/DropdownsRegistryList' description: OK headers: x-rate-limit-limit: description: The number of allowed requests in the current rate-limit period schema: type: integer x-rate-limit-remaining: description: The number of calls remaining in the current rate-limit period schema: type: integer x-rate-limit-reset: description: The number of seconds remaining in the current rate-limit period schema: type: integer '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request summary: List dropdowns for a given registry tags: - Registry /registries/{registry_id}/entity-schemas: get: deprecated: true description: List entity schemas by registry. Deprecated - use Schemas endpoints instead. operationId: listEntitySchemasByRegistry parameters: - description: ID for the registry in: path name: registry_id required: true schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/DeprecatedEntitySchemasList' description: OK '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request summary: List entity schemas by registry tags: - Registry /registries/{registry_id}/location-schemas: get: deprecated: true description: List location schemas by registry. Deprecated - use Schemas endpoints instead. operationId: listLocationSchemasByRegistry parameters: - description: ID for the registry in: path name: registry_id required: true schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/LocationSchemasList' description: OK '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request summary: List location schemas by registry tags: - Registry /registries/{registry_id}/plate-schemas: get: deprecated: true description: List plate schemas by registry. Deprecated - use Schemas endpoints instead. operationId: listPlateSchemasByRegistry parameters: - description: ID for the registry in: path name: registry_id required: true schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/PlateSchemasList' description: OK '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request summary: List plate schemas by registry tags: - Registry /registries/{registry_id}/registered-entities:bulk-get: get: description: Bulk get registered entities operationId: bulkGetRegisteredEntities parameters: - description: ID for the registry in: path name: registry_id required: true schema: type: string - description: Comma separated list of entity Registry IDs in: query name: entityRegistryIds required: true schema: type: string responses: '200': content: application/json: schema: $ref: '#/components/schemas/RegisteredEntitiesList' description: OK '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request '404': content: application/json: schema: $ref: '#/components/schemas/NotFoundError' description: Not Found summary: Bulk get registered entities tags: - Registry /registries/{registry_id}:bulk-register-entities: post: description: 'Attempts to move entities into the registry. Limit of 2500 entities per request. This endpoint will first check that the entities are all valid to be moved into the registry, given the namingStrategy. If any entities fail validation, no files will be moved and errors describing invalid entities is returned. If all entities pass validation, the entities are moved into the registry. ' operationId: registerEntities parameters: - description: ID for the registry in: path name: registry_id required: true schema: type: string requestBody: content: application/json: schema: $ref: '#/components/schemas/RegisterEntities' responses: '202': content: application/json: schema: $ref: '#/components/schemas/AsyncTaskLink' description: ' This endpoint launches a [long-running task](#/Tasks/getTask) and returns the Task ID of the launched task. When successful, the task has an empty response. Benchling cannot always process two registration attempts within the same registry at the same time, so it''s possible for the task to return an error response that indicates another attempt is already in progress and currently blocking this one. Benchling will automatically retry the task up to 3 times, and in the unlikely event that it is still failing, the task status will be "FAILED" and the error message will read: > Another registration attempt is in progress. Please try again in a few moments. If this problem persists, please wait 1-2 minutes before trying again. ' '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request summary: Register entities tags: - Registry /registries/{registry_id}:unregister-entities: post: description: Unregisters entities and moves them to a folder operationId: unregisterEntities parameters: - description: ID of the registry in: path name: registry_id required: true schema: type: string requestBody: content: application/json: schema: $ref: '#/components/schemas/UnregisterEntities' responses: '200': content: application/json: schema: $ref: '#/components/schemas/EmptyObject' description: OK '400': content: application/json: schema: $ref: '#/components/schemas/BadRequestError' description: Bad Request summary: Unregister entities tags: - Registry components: schemas: DeprecatedEntitySchemasList: properties: entitySchemas: items: $ref: '#/components/schemas/DeprecatedEntitySchema' readOnly: true type: array type: object Primer: properties: bases: readOnly: true type: string bindPosition: readOnly: true type: integer color: readOnly: true type: string end: description: 0-based exclusive end index. The end of the sequence is always represented as 0. type: integer name: readOnly: true type: string oligoId: type: string overhangLength: readOnly: true type: integer start: description: 0-based inclusive start index. type: integer strand: example: 1 type: integer type: object UnitSummary: properties: id: example: unit_NyKvCSBC type: string name: example: meter type: string symbol: example: m type: string unitTypeId: example: qnty_7W2R1EFJ type: string type: object ArchiveRecord: properties: reason: example: Made in error type: string type: object FieldType: enum: - dna_sequence_link - aa_sequence_link - custom_entity_link - entity_link - mixture_link - molecule_link - dropdown - part_link - translation_link - aa_part_link - base_molecule_link - blob_link - text - long_text - batch_link - storage_link - entry_link - assay_request_link - assay_result_link - assay_run_link - boolean - float - integer - datetime - date - json type: string MixtureWithEntityType: allOf: - $ref: '#/components/schemas/Mixture' - properties: entityType: enum: - mixture type: string type: object type: object ContainerLabels: properties: barcode: example: VIAL001 type: string id: example: cnt_12345 type: string name: example: My Container type: string type: object DropdownsRegistryList: properties: dropdowns: items: $ref: '#/components/schemas/DropdownSummary' type: array type: object DnaSequenceTranscription: properties: end: description: 0-based exclusive end index. The end of the sequence is always represented as 0. type: integer sequenceId: description: Linked RNA sequence ID. example: seq_VfVOART1 type: string start: description: 0-based inclusive start index. type: integer strand: example: 1 maximum: 1 minimum: -1 type: integer type: object FloatFieldDefinition: allOf: - $ref: '#/components/schemas/FieldDefinition' - properties: decimalPrecision: nullable: true type: number legalTextDropdownId: nullable: true type: string numericMax: nullable: true type: number numericMin: nullable: true type: number type: enum: - float type: string unit: allOf: - $ref: '#/components/schemas/UnitSummary' nullable: true type: object RegisterEntities: additionalProperties: false properties: entityIds: description: Array of entity IDs items: type: string maxItems: 2500 type: array namingStrategy: $ref: '#/components/schemas/NamingStrategy' required: - entityIds - namingStrategy type: object RnaSequenceWithEntityType: allOf: - $ref: '#/components/schemas/RnaSequence' - properties: entityType: enum: - rna_sequence type: string type: object type: object RegistrySchema: allOf: - $ref: '#/components/schemas/Schema' - properties: prefix: type: string registryId: type: string type: object NotFoundError: properties: error: allOf: - $ref: '#/components/schemas/BaseError' - properties: invalidId: type: string type: enum: - invalid_request_error type: string type: object Registry: properties: id: type: string modifiedAt: description: DateTime the Registry was last modified example: '2017-04-18T05:55:48.685345+00:00' format: date-time type: string name: type: string owner: $ref: '#/components/schemas/Organization' type: object MixtureMeasurementUnits: enum: - nL - uL - mL - L - g - kg - mg - ug - Units example: L nullable: true type: string AaSequence: properties: aliases: description: Array of aliases items: type: string type: array aminoAcids: description: Amino acids of the AA sequence. example: IKTATARRELAETSWTGDRLWGFSDNWAPALRRPSPSALGK type: string annotations: description: Array of annotation objects on the AA sequence. items: $ref: '#/components/schemas/AaAnnotation' type: array apiURL: description: The canonical url of the AA Sequence in the API. example: https://benchling.com/api/v2/aa-sequences/prtn_7nMBOMm0 format: uri readOnly: true type: string archiveRecord: allOf: - $ref: '#/components/schemas/ArchiveRecord' nullable: true authors: items: $ref: '#/components/schemas/UserSummary' type: array createdAt: description: DateTime the AA sequence was created. format: date-time readOnly: true type: string creator: $ref: '#/components/schemas/UserSummary' customFields: allOf: - $ref: '#/components/schemas/CustomFields' description: Custom fields set on the AA sequence. entityRegistryId: description: Registry ID of the AA sequence if registered. nullable: true type: string fields: $ref: '#/components/schemas/Fields' folderId: description: ID of the folder that contains the AA sequence. nullable: true type: string id: description: ID of the AA sequence. example: prtn_ObbdtGhC type: string length: description: Number of amino acids in the AA sequence. type: integer modifiedAt: description: DateTime the AA sequence was last modified. format: date-time readOnly: true type: string name: description: Name of the AA sequence. type: string registrationOrigin: allOf: - $ref: '#/components/schemas/RegistrationOrigin' nullable: true readOnly: true registryId: description: Registry the AA sequence is registered in. nullable: true type: string schema: allOf: - $ref: '#/components/schemas/SchemaSummary' nullable: true url: description: The path of the web URL, omitting the tenant domain type: string webURL: description: URL of the AA sequence. example: https://benchling.com/benchling/f/lib_55UxcIps-registry/prtn_7nMBOMm0-kedchain11/edit" format: uri readOnly: true type: string type: object RegisteredEntitiesList: properties: entities: items: $ref: '#/components/schemas/Entity' type: array type: object CustomEntity: properties: aliases: items: example: sBN000 type: string type: array apiURL: description: The canonical url of the Custom Entity in the API. example: https://benchling.com/api/v2/custom-entities/bfi_xCUXNVyG format: uri readOnly: true type: string archiveRecord: allOf: - $ref: '#/components/schemas/ArchiveRecord' nullable: true authors: items: $ref: '#/components/schemas/UserSummary' type: array createdAt: example: '2017-04-18T05:54:56.247545+00:00' format: date-time readOnly: true type: string creator: allOf: - $ref: '#/components/schemas/UserSummary' - readOnly: true customFields: $ref: '#/components/schemas/CustomFields' entityRegistryId: example: sBN000 nullable: true type: string fields: $ref: '#/components/schemas/Fields' folderId: example: lib_R8KcsjhW nullable: true type: string id: example: bfi_xCUXNVyG type: string modifiedAt: example: '2017-04-18T05:55:48.685345+00:00' format: date-time readOnly: true type: string name: example: sBN000 type: string registrationOrigin: allOf: - $ref: '#/components/schemas/RegistrationOrigin' nullable: true readOnly: true registryId: example: src_NetYd96a nullable: true type: string schema: allOf: - $ref: '#/components/schemas/SchemaSummary' example: id: ts_EM122lfJ name: Strain nullable: true url: description: The path of the web URL, omitting the tenant domain type: string webURL: example: https://benchling.com/benchling/f/R8KcsjhW-academic-registry/bfi-xCUXNVyG-sbn000/edit readOnly: true type: string type: object UnregisterEntities: additionalProperties: false properties: entityIds: description: Array of entity IDs items: type: string type: array folderId: description: ID of the folder that the entities should be moved to type: string required: - entityIds - folderId type: object RnaOligoWithEntityType: allOf: - $ref: '#/components/schemas/RnaOligo' - properties: entityType: enum: - rna_oligo type: string type: object type: object AaSequenceWithEntityType: allOf: - $ref: '#/components/schemas/AaSequence' - properties: entityType: enum: - aa_sequence type: string type: object type: object SimpleFieldDefinition: allOf: - $ref: '#/components/schemas/FieldDefinition' - properties: type: enum: - dna_sequence_link - aa_sequence_link - custom_entity_link - mixture_link - molecule_link - blob_link - text - long_text - boolean - datetime - date - json type: string type: object RnaSequencePart: allOf: - $ref: '#/components/schemas/NucleotideSequencePart' - properties: strand: example: 1 maximum: 1 minimum: 1 type: integer type: object EntitySchema: allOf: - $ref: '#/components/schemas/RegistrySchema' - properties: constraint: nullable: true properties: fieldDefinitionNames: items: type: string type: array hasUniqueResidues: type: boolean type: object containableType: enum: - NONE - ENTITY - BATCH type: string containerNameTemplateParts: items: $ref: '#/components/schemas/NameTemplatePart' nullable: true type: array modifiedAt: description: DateTime the Entity Schema was last modified example: '2017-04-18T05:55:48.685345+00:00' format: date-time type: string nameTemplateParts: items: $ref: '#/components/schemas/NameTemplatePart' nullable: true type: array type: enum: - custom_entity - dna_sequence - rna_sequence - aa_sequence - mixture - dna_oligo - rna_oligo - molecule readOnly: true type: string type: object title: EntitySchema CustomEntityWithEntityType: allOf: - $ref: '#/components/schemas/CustomEntity' - properties: entityType: enum: - custom_entity type: string type: object type: object CustomField: properties: value: type: string type: object EmptyObject: type: object SequenceFeatureCustomField: description: A name and value pair associated with a sequence feature (annotation or translation). For genbank imports, these are the qualifiers associated with each feature. properties: name: description: Name of the custom field type: string value: description: Value of the custom field type: string type: object Entity: discriminator: mapping: aa_sequence: '#/components/schemas/AaSequenceWithEntityType' custom_entity: '#/components/schemas/CustomEntityWithEntityType' dna_oligo: '#/components/schemas/DnaOligoWithEntityType' dna_sequence: '#/components/schemas/DnaSequenceWithEntityType' mixture: '#/components/schemas/MixtureWithEntityType' molecule: '#/components/schemas/MoleculeWithEntityType' rna_oligo: '#/components/schemas/RnaOligoWithEntityType' rna_sequence: '#/components/schemas/RnaSequenceWithEntityType' propertyName: entityType oneOf: - $ref: '#/components/schemas/DnaSequenceWithEntityType' - $ref: '#/components/schemas/RnaSequenceWithEntityType' - $ref: '#/components/schemas/AaSequenceWithEntityType' - $ref: '#/components/schemas/MixtureWithEntityType' - $ref: '#/components/schemas/DnaOligoWithEntityType' - $ref: '#/components/schemas/RnaOligoWithEntityType' - $ref: '#/components/schemas/MoleculeWithEntityType' - $ref: '#/components/schemas/CustomEntityWithEntityType' type: object AaAnnotation: properties: color: type: string end: description: 0-based exclusive end index. The end of the AA sequence is always represented as 0. type: integer id: example: prtnann_o7zMPG0P type: string name: maxLength: 255 type: string notes: example: Cong et al Science. 2013 Jan 3. maxLength: 10000 type: string start: description: 0-based inclusive start index. type: integer type: example: Site maxLength: 255 type: string type: object SequenceFeatureBase: properties: color: description: Hex color code used when displaying this feature in the UI. example: '#F58A5E' type: string customFields: items: $ref: '#/components/schemas/SequenceFeatureCustomField' maxItems: 100 type: array name: maxLength: 2048 type: string notes: example: Cong et al Science. 2013 Jan 3. maxLength: 10000 type: string type: object IngredientMeasurementUnits: enum: - nL - uL - mL - L - mg - g - kg - ug - Units - Cells - mol - mmol - umol example: mL nullable: true type: string RegistriesList: properties: registries: items: $ref: '#/components/schemas/Registry' type: array type: object AsyncTaskLink: properties: taskId: type: string type: object RnaSequence: properties: aliases: items: type: string type: array alignmentIds: description: API IDs of Nucleotide Alignments involving the RNA sequence items: type: string type: array annotations: items: $ref: '#/components/schemas/RnaAnnotation' type: array apiURL: description: The canonical url of the RNA Sequence in the API. example: https://benchling.com/api/v2/rna-sequences/seq_asZya4lk format: uri readOnly: true type: string archiveRecord: allOf: - $ref: '#/components/schemas/ArchiveRecord' nullable: true authors: items: $ref: '#/components/schemas/UserSummary' type: array bases: type: string createdAt: format: date-time readOnly: true type: string creator: $ref: '#/components/schemas/UserSummary' customFields: $ref: '#/components/schemas/CustomFields' customNotation: description: Representation of the RNA Sequence in the custom notation specified in the request. Null if no notation was specified. nullable: true type: string customNotationName: description: Name of the custom notation specified in the request. Null if no notation was specified. nullable: true type: string entityRegistryId: nullable: true type: string fields: $ref: '#/components/schemas/Fields' folderId: nullable: true type: string helm: description: Representation of the RNA Sequence in HELM syntax, including any chemical modifications. example: RNA1{r(A)p.r(C)[Ssp].r(U)p.r(U)p.r(U)p.r(U)p.r(U)p}$$$$V2.0 nullable: true type: string id: type: string isCircular: example: false type: boolean length: type: integer modifiedAt: format: date-time readOnly: true type: string name: type: string parts: items: $ref: '#/components/schemas/RnaSequencePart' type: array primers: items: $ref: '#/components/schemas/Primer' type: array registrationOrigin: allOf: - $ref: '#/components/schemas/RegistrationOrigin' nullable: true readOnly: true registryId: nullable: true type: string schema: allOf: - $ref: '#/components/schemas/SchemaSummary' nullable: true translations: items: $ref: '#/components/schemas/Translation' type: array url: description: The path of the web URL, omitting the tenant domain type: string webURL: readOnly: true type: string type: object RnaAnnotation: allOf: - $ref: '#/components/schemas/SequenceFeatureBase' - properties: end: description: 0-based exclusive end index. The end of the sequence is always represented as 0. type: integer start: description: 0-based inclusive start index. type: integer strand: example: 1 maximum: 1 minimum: 0 type: integer type: type: string type: object DnaSequence: properties: aliases: items: type: string type: array annotations: items: $ref: '#/components/schemas/DnaAnnotation' type: array apiURL: description: The canonical url of the DNA Sequence in the API. example: https://benchling.com/api/v2/dna-sequences/seq_asQya4lk format: uri readOnly: true type: string archiveRecord: allOf: - $ref: '#/components/schemas/ArchiveRecord' nullable: true authors: items: $ref: '#/components/schemas/UserSummary' type: array bases: type: string createdAt: format: date-time readOnly: true type: string creator: $ref: '#/components/schemas/UserSummary' customFields: $ref: '#/components/schemas/CustomFields' dnaAlignmentIds: description: API IDs of Nucleotide Alignments involving the RNA sequence items: type: string type: array entityRegistryId: nullable: true type: string fields: $ref: '#/components/schemas/Fields' folderId: nullable: true type: string id: type: string isCircular: type: boolean length: type: integer modifiedAt: format: date-time readOnly: true type: string name: type: string parts: items: $ref: '#/components/schemas/DnaSequencePart' type: array primers: items: $ref: '#/components/schemas/Primer' type: array registrationOrigin: allOf: - $ref: '#/components/schemas/RegistrationOrigin' nullable: true readOnly: true registryId: nullable: true type: string schema: allOf: - $ref: '#/components/schemas/SchemaSummary' nullable: true transcriptions: items: $ref: '#/components/schemas/DnaSequenceTranscription' type: array translations: items: $ref: '#/components/schemas/Translation' type: array url: description: The path of the web URL, omitting the tenant domain type: string webURL: readOnly: true type: string type: object ContainerSchemasList: properties: containerSchemas: items: $ref: '#/components/schemas/ContainerSchema' readOnly: true type: array type: object SchemaSummary: properties: id: type: string name: type: string type: object ContainerSchema: allOf: - $ref: '#/components/schemas/RegistrySchema' - properties: modifiedAt: description: DateTime the Container Schema was last modified example: '2017-04-18T05:55:48.685345+00:00' format: date-time type: string type: enum: - container readOnly: true type: string type: object DeprecatedEntitySchema: allOf: - $ref: '#/components/schemas/EntitySchema' - properties: type: enum: - custom_entity - dna_sequence - aa_sequence - mixture - dna_oligo - rna_oligo - molecule - entry readOnly: true type: string type: object Molecule: additionalProperties: false properties: aliases: description: Array of aliases. items: type: string type: array apiURL: description: The canonical url of the Molecule in the API. format: uri readOnly: true type: string archiveRecord: allOf: - $ref: '#/components/schemas/ArchiveRecord' nullable: true authors: items: $ref: '#/components/schemas/UserSummary' type: array canonicalizedSmiles: description: The canonicalized chemical structure in SMILES format. example: Nc1nc(=O)n([H])cc1C1CC1 type: string createdAt: description: DateTime the Molecule was created. format: date-time readOnly: true type: string creator: $ref: '#/components/schemas/UserSummary' customFields: allOf: - $ref: '#/components/schemas/CustomFields' description: Custom fields set on the Molecule. entityRegistryId: description: Registry ID of the Molecule if registered. nullable: true type: string fields: $ref: '#/components/schemas/Fields' folderId: description: ID of the folder that contains the Molecule. nullable: true type: string id: description: ID of the Molecule. example: mol_bhuDUw9D type: string modifiedAt: description: DateTime the Molecule was last modified. format: date-time readOnly: true type: string name: description: Name of the Molecule. type: string originalSmiles: description: The original chemical structure supplied by the user in SMILES format. Null if the user did not originally supply SMILES. example: Nc1nc(=O)n([H])cc1C1CC1 nullable: true type: string registrationOrigin: allOf: - $ref: '#/components/schemas/RegistrationOrigin' nullable: true readOnly: true registryId: description: Registry the Molecule is registered in. nullable: true type: string schema: allOf: - $ref: '#/components/schemas/SchemaSummary' nullable: true webURL: description: URL of the Molecule. example: https://benchling.com/benchling/f/lib_R8KcsjhW-molecules/mol_xCUXNVyG-molecule1/edit format: uri readOnly: true type: string type: object BoxSchema: allOf: - $ref: '#/components/schemas/RegistrySchema' - properties: containerSchema: nullable: true properties: id: type: string name: type: string type: object height: type: number modifiedAt: description: DateTime the Box Schema was last modified example: '2017-04-18T05:55:48.685345+00:00' format: date-time type: string type: enum: - box readOnly: true type: string width: type: number type: object LocationSchema: allOf: - $ref: '#/components/schemas/RegistrySchema' - properties: modifiedAt: description: DateTime the Location Schema was last modified example: '2017-04-18T05:55:48.685345+00:00' format: date-time type: string type: enum: - location readOnly: true type: string type: object DnaSequenceWithEntityType: allOf: - $ref: '#/components/schemas/DnaSequence' - properties: entityType: enum: - dna_sequence type: string type: object type: object Fields: additionalProperties: $ref: '#/components/schemas/Field' type: object NucleotideSequencePart: properties: end: description: 0-based exclusive end index. The end of the sequence is always represented as 0. type: integer sequenceId: example: seq_VfVOART1 type: string start: description: 0-based inclusive start index. type: integer type: object DnaOligoWithEntityType: allOf: - $ref: '#/components/schemas/DnaOligo' - properties: entityType: enum: - dna_oligo type: string type: object type: object BaseError: properties: message: type: string type: type: string userMessage: type: string type: object PlateSchemasList: properties: plateSchemas: items: $ref: '#/components/schemas/PlateSchema' readOnly: true type: array type: object RnaOligo: allOf: - $ref: '#/components/schemas/Oligo' - properties: annotations: description: Annotations on the Oligo. items: $ref: '#/components/schemas/RnaAnnotation' type: array apiURL: example: https://benchling.com/api/v2/rna-oligos/seq_bhuDUw9D type: string bases: example: ACUUUUU type: string customNotation: description: Representation of the oligo in the custom notation specified in the request. Null if no notation was specified. nullable: true type: string customNotationName: description: Name of the custom notation specified in the request. Null if no notation was specified. nullable: true type: string helm: description: Representation of the oligo in HELM syntax, including any chemical modifications example: RNA1{r(A)p.r(C)[Ssp].r(U)p.r(U)p.r(U)p.r(U)p.r(U)p}$$$$V2.0 type: string nucleotideType: example: RNA type: string DropdownSummary: properties: id: description: ID of the dropdown type: string name: description: Name of the dropdown type: string type: object MoleculeWithEntityType: allOf: - $ref: '#/components/schemas/Molecule' - properties: entityType: enum: - molecule type: string type: object type: object NamingStrategy: description: 'Specifies the behavior for automatically generated names when registering an entity. - NEW_IDS: Generate new registry IDs - IDS_FROM_NAMES: Generate registry IDs based on entity names - DELETE_NAMES: Generate new registry IDs and replace name with registry ID - SET_FROM_NAME_PARTS: Generate new registry IDs, rename according to name template, and keep old name as alias - REPLACE_NAMES_FROM_PARTS: Generate new registry IDs, and replace name according to name template - KEEP_NAMES: Keep existing entity names as registry IDs - REPLACE_ID_AND_NAME_FROM_PARTS: Generate registry IDs and names according to name template ' enum: - NEW_IDS - IDS_FROM_NAMES - DELETE_NAMES - SET_FROM_NAME_PARTS - REPLACE_NAMES_FROM_PARTS - KEEP_NAMES - REPLACE_ID_AND_NAME_FROM_PARTS type: string BatchSchema: allOf: - $ref: '#/components/schemas/RegistrySchema' - properties: entitySchemaId: type: string modifiedAt: description: DateTime the Batch Schema was last modified example: '2017-04-18T05:55:48.685345+00:00' format: date-time type: string type: object DropdownFieldDefinition: allOf: - $ref: '#/components/schemas/FieldDefinition' - properties: dropdownId: nullable: true type: string type: enum: - dropdown type: string type: object PartySummary: properties: handle: type: string id: type: string name: type: string type: object DnaSequencePart: allOf: - $ref: '#/components/schemas/NucleotideSequencePart' - properties: strand: example: 1 maximum: 1 minimum: -1 type: integer type: object LocationSchemasList: properties: locationSchemas: items: $ref: '#/components/schemas/LocationSchema' readOnly: true type: array type: object CustomFields: additionalProperties: $ref: '#/components/schemas/CustomField' example: Legacy ID: value: STR100 type: object Organization: properties: handle: type: string id: type: string name: type: string type: object FieldDefinition: properties: archiveRecord: allOf: - $ref: '#/components/schemas/ArchiveRecord' nullable: true id: example: tsf_HXUnClU9 type: string isMulti: type: boolean isRequired: type: boolean name: example: Resistance Gene type: string type: $ref: '#/components/schemas/FieldType' type: object BatchSchemasList: properties: batchSchemas: items: $ref: '#/components/schemas/BatchSchema' readOnly: true type: array type: object SchemaLinkFieldDefinition: allOf: - $ref: '#/components/schemas/FieldDefinition' - properties: schemaId: nullable: true type: string type: enum: - entity_link - entry_link - part_link - translation_link - batch_link - storage_link - assay_request_link - assay_result_link - assay_run_link type: string type: object EntityLabels: properties: entityRegistryId: example: REAG000 nullable: true type: string id: example: bfi_12345 type: string name: example: Deionized Water type: string type: object BoxSchemasList: properties: boxSchemas: items: $ref: '#/components/schemas/BoxSchema' readOnly: true type: array type: object BadRequestError: properties: error: allOf: - $ref: '#/components/schemas/BaseError' - properties: type: enum: - invalid_request_error type: string type: object DnaAnnotation: allOf: - $ref: '#/components/schemas/SequenceFeatureBase' - properties: end: description: 0-based exclusive end index. The end of the sequence is always represented as 0. type: integer start: description: 0-based inclusive start index. type: integer strand: maximum: 1 minimum: -1 type: integer type: type: string type: object IntegerFieldDefinition: allOf: - $ref: '#/components/schemas/FieldDefinition' - properties: numericMax: nullable: true type: number numericMin: nullable: true type: number type: enum: - integer type: string unit: allOf: - $ref: '#/components/schemas/UnitSummary' nullable: true type: object DnaOligo: allOf: - $ref: '#/components/schemas/Oligo' - properties: annotations: description: Annotations on the Oligo. items: $ref: '#/components/schemas/DnaAnnotation' type: array apiURL: example: https://benchling.com/api/v2/dna-oligos/seq_bhuDUw9D type: string bases: example: ACTTTTT type: string customNotation: description: Representation of the oligo in the custom notation specified in the request. Null if no notation was specified. nullable: true type: string customNotationName: description: Name of the custom notation specified in the request. Null if no notation was specified. nullable: true type: string helm: description: Representation of the oligo in HELM syntax, including any chemical modifications example: RNA1{d(A)p.d(C)[Ssp].d(T)p.d(T)p.d(T)p.d(T)p.d(T)p}$$$$V2.0 type: string Schema: properties: archiveRecord: allOf: - $ref: '#/components/schemas/ArchiveRecord' nullable: true fieldDefinitions: items: oneOf: - $ref: '#/components/schemas/SimpleFieldDefinition' - $ref: '#/components/schemas/IntegerFieldDefinition' - $ref: '#/components/schemas/FloatFieldDefinition' - $ref: '#/components/schemas/DropdownFieldDefinition' - $ref: '#/components/schemas/SchemaLinkFieldDefinition' type: array id: type: string name: type: string type: type: string type: object UserSummary: allOf: - $ref: '#/components/schemas/PartySummary' - example: handle: lpasteur id: ent_a0SApq3z name: Louis Pasteur Mixture: properties: aliases: items: example: FRM000 type: string type: array allowMeasuredIngredients: description: Derived from the mixture's schema. readOnly: true type: boolean amount: description: The positive numerical amount value of this mixture in string format (to preserve full precision). Pair with `units`. Supports scientific notation (1.23e4). example: '123' type: string apiURL: description: The canonical url of the Mixture in the API. example: https://benchling.com/api/v2/mixtures/mxt_xCUXNVyG format: uri readOnly: true type: string archiveRecord: allOf: - $ref: '#/components/schemas/ArchiveRecord' nullable: true authors: items: $ref: '#/components/schemas/UserSummary' type: array createdAt: example: '2017-04-18T05:54:56.247545+00:00' format: date-time readOnly: true type: string creator: allOf: - $ref: '#/components/schemas/UserSummary' - readOnly: true customFields: $ref: '#/components/schemas/CustomFields' entityRegistryId: example: FRM000 nullable: true type: string fields: allOf: - $ref: '#/components/schemas/Fields' description: Mixtures can have up to one parent mixture field. folderId: example: lib_R8KcsjhW nullable: true type: string id: example: mxt_xCUXNVyG type: string ingredients: description: List of ingredients on this mixture. items: $ref: '#/components/schemas/Ingredient' type: array modifiedAt: example: '2017-04-18T05:55:48.685345+00:00' format: date-time readOnly: true type: string name: example: FRM000 type: string registrationOrigin: allOf: - $ref: '#/components/schemas/RegistrationOrigin' nullable: true readOnly: true registryId: example: src_NetYd96a nullable: true type: string schema: allOf: - $ref: '#/components/schemas/SchemaSummary' example: id: ts_EM122lfJ name: Prep units: $ref: '#/components/schemas/MixtureMeasurementUnits' webURL: example: https://benchling.com/benchling/f/R8KcsjhW-academic-registry/mxt-xCUXNVyG-sbn000/edit readOnly: true type: string type: object Translation: allOf: - $ref: '#/components/schemas/SequenceFeatureBase' - properties: aminoAcids: readOnly: true type: string coerceStartCodonToMethionine: default: false description: Whether to override the translation of the start codon to Methionine. Has no effect when the start codon already translates to Methionine. type: boolean end: description: 0-based exclusive end index. The end of the sequence is always represented as 0. type: integer geneticCode: default: STANDARD description: The genetic code to use when translating the nucleotide sequence into amino acids. enum: - STANDARD - VERTEBRATE_MITOCHONDRIAL - YEAST_MITOCHONDRIAL - MOLD_PROTOZOAN_COELENTERATE_MITOCHONDRIAL_MYCOPLASMA_SPIROPLASMA - INVERTEBRATE_MITOCHONDRIAL - CILIATE_DASYCLADACEAN_HEXAMITA_NUCLEAR - ECHINODERM_FLATWORM_MITOCHONDRIAL - EUPLOTID_NUCLEAR - BACTERIAL_ARCHAEAL_PLANT_PLASTID - ALTERNATIVE_YEAST_NUCLEAR - ASCIDIAN_MITOCHONDRIAL - ALTERNATIVE_FLATWORM_MITOCHONDRIAL - CHLOROPHYCEAN_MITOCHONDRIAL - TREMATODE_MITOCHONDRIAL - SCENEDESMUS_OBLIQUUS_MITOCHONDRIAL - THRAUSTOCHYTRIUM_MITOCHONDRIAL - RHABDOPLEURIDAE_MITOCHONDRIAL - CANDIDATE_DIVISION_SR1_GRACILIBACTERIA - PACHYSOLEN_TANNOPHILUS_NUCLEAR - MESODINIUM_NUCLEAR - PERITRICH_NUCLEAR - CEPHALODISCIDAE_MITOCHONDRIAL_UAA_TYR type: string regions: items: properties: end: description: 0-based exclusive end index. The end of the sequence is always represented as 0. type: integer start: description: 0-based inclusive start index. type: integer type: object type: array start: description: 0-based inclusive start index. type: integer strand: example: 1 type: integer type: object Field: properties: displayValue: nullable: true readOnly: true type: string isMulti: readOnly: true type: boolean textValue: example: Amp nullable: true readOnly: true type: string type: allOf: - $ref: '#/components/schemas/FieldType' readOnly: true value: description: 'For single link fields, use the id of the item you want to link (eg. "seq_jdf8BV24"). For multi-link fields, use an array of ids of the items you want to link (eg. ["seq_jdf8BV24"]) ' nullable: true oneOf: - type: string - type: boolean - type: number - type: object - items: type: string type: array required: - value type: object PlateSchema: allOf: - $ref: '#/components/schemas/RegistrySchema' - properties: containerSchema: nullable: true properties: id: type: string name: type: string type: object height: type: number modifiedAt: description: DateTime the Plate Schema was last modified example: '2017-04-18T05:55:48.685345+00:00' format: date-time type: string plateType: type: string type: enum: - plate readOnly: true type: string width: type: number type: object NameTemplatePart: properties: datetimeFormat: nullable: true type: string fieldId: nullable: true type: string text: nullable: true type: string type: type: string type: object Oligo: discriminator: mapping: DNA: DnaOligo RNA: RnaOligo propertyName: nucleotideType properties: aliases: description: Array of aliases items: type: string type: array apiURL: description: The canonical url of the Oligo in the API. format: uri readOnly: true type: string archiveRecord: allOf: - $ref: '#/components/schemas/ArchiveRecord' nullable: true authors: items: $ref: '#/components/schemas/UserSummary' type: array bases: description: Base pairs of the Oligo. example: ACTTTTT type: string createdAt: description: DateTime the Oligo was created. format: date-time readOnly: true type: string creator: $ref: '#/components/schemas/UserSummary' customFields: allOf: - $ref: '#/components/schemas/CustomFields' description: Custom fields set on the Oligo. entityRegistryId: description: Registry ID of the Oligo if registered. nullable: true type: string fields: $ref: '#/components/schemas/Fields' folderId: description: ID of the folder that contains the Oligo. nullable: true type: string id: description: ID of the Oligo. example: seq_bhuDUw9D type: string length: description: Number of bases in the Oligo. type: integer modifiedAt: description: DateTime the Oligo was last modified. format: date-time readOnly: true type: string name: description: Name of the Oligo. type: string nucleotideType: description: Nucleotide type of the Oligo. enum: - DNA - RNA type: string registrationOrigin: allOf: - $ref: '#/components/schemas/RegistrationOrigin' nullable: true readOnly: true registryId: description: Registry the Oligo is registered in. nullable: true type: string schema: allOf: - $ref: '#/components/schemas/SchemaSummary' nullable: true webURL: description: URL of the Oligo. example: https://benchling.com/benchling/f/lib_hBHqKbzE-oligos/seq_bhuDUw9D-test-oligo-abc/edit format: uri readOnly: true type: string type: object RegistrationOrigin: properties: originEntryId: nullable: true readOnly: true type: string registeredAt: format: date-time readOnly: true type: string type: object Ingredient: properties: amount: description: 'The amount value of this ingredient in its mixture, in string format (to preserve full precision). Pair with `units`. Supports scientific notation (1.23e4). One ingredient on this mixture can have an amount value of `"QS"`. ' example: '12' nullable: true type: string catalogIdentifier: example: DION_004 nullable: true type: string componentEntity: allOf: - $ref: '#/components/schemas/EntityLabels' - description: The entity that uniquely identifies this component. componentLotContainer: allOf: - $ref: '#/components/schemas/ContainerLabels' description: The container representing the component lot for this ingredient. This is only present if the mixture schema supports component lots in "inventory" format. nullable: true componentLotEntity: allOf: - $ref: '#/components/schemas/EntityLabels' description: The entity representing the component lot for this ingredient. This is only present if the mixture schema supports component lots in "inventory" format. nullable: true componentLotText: description: Text representing the component lot for this ingredient. This is only present if the mixture schema supports component lots in "text" format. example: DION_004-source_001 nullable: true type: string hasParent: type: boolean notes: nullable: true type: string targetAmount: description: The target amount for this ingredient such that this ingredient's proportion in its mixture would preserve the equivalent ingredient's proportion in the parent mixture. Pair with `units`. example: '123' nullable: true readOnly: true type: string units: $ref: '#/components/schemas/IngredientMeasurementUnits' 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: /api/v2/token type: oauth2 externalDocs: description: Additional API Documentation url: https://docs.benchling.com