--- title: "Batch update RnaSequence" method: PATCH path: "/api/v3/rna-sequence:batch-update" tags: ["RNA Sequence"] --- # Batch update RnaSequence `PATCH /api/v3/rna-sequence:batch-update` ## Request - Base URL: `https://{tenant_name}.benchling.com` - URL: `https://{tenant_name}.benchling.com/api/v3/rna-sequence:batch-update` - Auth: HTTP bearer Batch update RNA sequences synchronously in one transaction. Maximum 25 items per request. Each item follows the same field requirements and archive constraints as the single-update endpoint. If any item fails validation, the transaction fails and no RNA sequences are updated. ## Request body - object - `items` UpdateRnaSequenceInputWithPathParams[], required - `aliases` string[]: Array of aliases - `allowCustomFieldDeletion` boolean: When true, custom fields present on the entity but omitted from the update payload will be deleted. When false or omitted, omitting existing custom fields is an error. Defaults to false. - `annotations` RnaAnnotationInput[]: Annotations on the RNA sequence, not including translations or primers. Annotations on parts are not included. - `color` string: Hex color when displaying the annotation. A random color is assigned if omitted. - `customFields` CustomFieldInput[]: Custom fields on the annotation. Each field name may be at most 1024 characters and each value at most 100000 characters. - `name` string, required: Name of the custom field. - `value` string: Value of the custom field. Defaults to an empty string if omitted. - `end` integer, required: 0-based exclusive end index. For ranges ending at the sequence end, API responses return `sequenceLength`, never `0`. On input, `sequenceLength` or `0` may be used. - `name` string, required: Name of the annotation. - `notes` string: Text notes on the annotation. Defaults to an empty string if omitted. - `start` integer, required: 0-based inclusive start index. - `type` string: Feature type of the annotation. - `archiveReason` string: Why it is being archived. Required when `archived` is `true`, and not allowed when unarchiving. - `archived` boolean: Set to `true` to archive or `false` to unarchive it. Archiving requires `archiveReason`. - `authorIds` string[] - `bases` string: Bases of the RNA sequence. Mutually exclusive with `helm` and `customNotation`. - `customFields` object: Custom fields set on the RNA sequence. - `customNotation` string, nullable: Sequence in a vendor-specific custom notation syntax. Requires custom syntaxes to be enabled. When `customNotation` is set, `customNotationId` is required. Mutually exclusive with `bases` and `helm`. - `customNotationId` string, nullable: ID of the custom notation syntax used to interpret `customNotation`. When `customNotation` is set, `customNotationId` is required; omit both when using `bases` or `helm`. - `entityRegistryId` string: Registry ID to assign to the entity. When registering, specifying this value sets the registry ID of the entity. When already registered, specifying this value updates the entity's registry ID. If set, naming_strategy must be unspecified. - `folderId` string - `helm` string: HELM notation for the RNA sequence and chemical modifications. Requires the modified nucleotides feature to be enabled. Mutually exclusive with `bases` and `customNotation`. - `id` string, required: API identifier of the registry item to update. - `name` string: Name of the item. - `namingStrategy` 'NEW_IDS' | 'IDS_FROM_NAMES' | 'DELETE_NAMES' | 'SET_FROM_NAME_PARTS' | 'REPLACE_NAMES_FROM_PARTS' | 'KEEP_NAMES' | 'REPLACE_ID_AND_NAME_FROM_PARTS': Strategy to use for labeling the item in the registry if registering. If one is specified, the entity_registry_id must be unspecified. - `parts` RnaPartInput[]: Part features linking regions of this sequence to other RNA sequences. - `end` integer, required: 0-based exclusive end index. For ranges ending at the sequence end, API responses return `sequenceLength`, never `0`. On input, `sequenceLength` or `0` may be used. - `sequenceId` string, required: RNA sequence this part refers to. - `start` integer, required: 0-based inclusive start index. - `primers` PrimerInput[]: Primer bind features on the RNA sequence. Primers on parts are not included. - `location` union, required - object: bind_and_overhang variant - `locationType` 'bind_and_overhang', required: Discriminator for primer binding location. Use `start_and_end` for start/end coordinates, or `bind_and_overhang` for bind position and overhang length. - `bindPosition` integer, required: 0-based index of the base at the 3' end of the binding region. - `overhangLength` integer, required: Number of 5' primer bases that are not part of the binding region. - object: start_and_end variant - `locationType` 'start_and_end', required: Discriminator for primer binding location. Use `start_and_end` for start/end coordinates, or `bind_and_overhang` for bind position and overhang length. - `end` integer, required: 0-based exclusive end of the binding region. For ranges ending at the sequence end, API responses return `sequenceLength`, never `0`. On input, `sequenceLength` or `0` may be used. - `start` integer, required: 0-based inclusive start of the binding region. - `oligoId` string, required: Linked Oligo entity, which holds the name, bases, and color for this primer bind site. - `strand` 'FORWARD' | 'REVERSE', required: Strand for this primer; `FORWARD` or `REVERSE`. - `registryId` string, nullable: A not null value means the entity should be registered. A null value means it should be unregistered. If not null, the value must match the registry of the item's schema. - `schemaFields` object - `schemaId` string - `translations` RnaTranslationInput[]: Translation annotations present on the RNA sequence. Translations may be one region or split across multiple regions. Translations on parts are not included. - `color` string: Hex color when displaying the translation. Defaults to light blue (`#84B0DC`) if omitted. - `customFields` CustomFieldInput[]: Custom fields on the translation. - `name` string, required: Name of the custom field. - `value` string: Value of the custom field. Defaults to an empty string if omitted. - `geneticCode` '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': Genetic code for the translation. Defaults to `STANDARD` if omitted. Genetic codes with ambiguous stop codons are not supported: `BLASTOCRITHIDIA_NUCLEAR`, `CONDYLOSTOMA_NUCLEAR`, `KARYORELICT_NUCLEAR`. - `name` string: Name of the translation. - `notes` string: Text notes on the translation. Defaults to an empty string if omitted. - `regions` TranslationRegionInput[], required: Array of regions to translate. For single-region translations, provide one element. - `end` integer, required: 0-based exclusive end index. For ranges ending at the sequence end, API responses return `sequenceLength`, never `0`. On input, `sequenceLength` or `0` may be used. - `start` integer, required: 0-based inclusive start index. - `translateFirstCodonToMethionine` boolean: Whether or not the first codon has been forced to be translated as methionine. Defaults to false if omitted. ## Response `200` OK - RnaSequenceBatchupdateResponse200 - `items` RnaSequence[], required - `__typename` string - `aliases` string[], nullable: Array of aliases - `annotations` string, uri: Annotations on the RNA sequence, not including translations or primers. Annotations on parts are not included. - `archiveReason` string, nullable - `archived` boolean - `bases` string: Bases of the RNA sequence. - `canonicalHelm` string: Normalized HELM notation for this RNA sequence. - `createdAt` string, datetime, nullable - `customFields` CustomField[], nullable: Custom fields set on the RNA sequence. - `__typename` string - `name` string, nullable - `value` string, nullable - `entityRegistryId` string, nullable: The registry-assigned identifier for this item (e.g. its registry ID shown in the UI), present only once the item has been registered. Null if the item is not registered. - `folder` FolderRef - `__typename` string - `id` string, api_id - `id` string - `modifiedAt` string, datetime, nullable - `modifiedNucleotides` string, uri: Modifications applied to this RNA sequence. - `name` string: Name of the item. - `nucleotideAlignments` string, uri: Nucleotide alignments that use this sequence as the reference sequence. For template alignments, this is the template sequence; for consensus alignments, this is the derived consensus sequence. - `parts` string, uri: Part features linking regions of this sequence to other RNA sequences. - `primers` string, uri: Primer bind features on the RNA sequence. Primers on parts are not included. - `project` ProjectRef - `__typename` string - `id` string, api_id - `registrationOrigin` RegistrationOrigin: Captures the provenance of an entity's registration into the registry. The `originEntry` links to the `DocumentLike` (typically an entry or notebook) from which the entity was registered, providing traceability back to the original experimental context. The `registeredAt` timestamp records when the registration occurred. This information helps scientists understand where registered entities came from and when they were added to the registry. - `__typename` string - `originEntry` DocumentLikeRef - `__typename` string - `id` string, api_id - `registeredAt` string, datetime, nullable - `registry` RegistryRef - `__typename` string - `id` string, api_id - `schema` EntitySchemaRef - `__typename` string - `id` string, api_id - `translations` string, uri: Translation annotations present on the RNA sequence. Translations may be one region or split across multiple regions. Translations on parts are not included. - `typedSchema` RnaSequenceSchemaRef - `__typename` string - `id` string, api_id - `authors` string, uri, nullable - `creator` PrincipalRef - `__typename` string - `id` string, api_id - `schemaFields` SchemaFieldValue[], nullable - `__typename` string - `fieldDefinition` SchemaFieldDefinitionRef - `__typename` string - `id` string, api_id - `id` string - `linkedEntityId` string, nullable - `value` union: Types of values that Benchling can interpret. - object: A type that represents a list of BenchlingValues, used for multi-value cells (e.g. alias columns). - `__typename` 'ArrayValue', required: Discriminator value: ArrayValue - `value` SingularBenchlingValue[] - union: A union of value types that can appear as elements within an ArrayValue. Identical to BenchlingValue but excludes ArrayValue to prevent nesting. Keep in sync with BenchlingValue. - … - object: A type that represents boolean values. - `__typename` 'BooleanValue', required: Discriminator value: BooleanValue - `value` boolean: The boolean value. - object: A type that represents datetime values. - `__typename` 'DateTimeValue', required: Discriminator value: DateTimeValue - `value` string, datetime: The datetime value with UTC as the timezone. - object: A type that represents date values. - `__typename` 'DateValue', required: Discriminator value: DateValue - `value` string, date: The date value. - object: A type that represents decimal value as strings. - `__typename` 'DecimalValue', required: Discriminator value: DecimalValue - `numericValue` number, double, nullable: Deprecated. The float representation of the decimal value. - `value` string, nullable: The decimal value in a string representation - object: A type that represents integer values. - `__typename` 'IntegerValue', required: Discriminator value: IntegerValue - `value` integer: The integer value. - object: A type that represents JSON values. - `__typename` 'JsonValue', required: Discriminator value: JsonValue - `value` union: The JSON value. - object - string[] - string - number, double - boolean - object: A type that represents a list of links to other objects. - `__typename` 'ObjectLinkListValue', required: Discriminator value: ObjectLinkListValue - `value` LinkableDomainObject[]: The list of objects that this value links to. Inaccessible objects may be returned instead if the object is not found with the current permission set. - union: A union representing items that can be linked to. If you have a type that can be linked to, it can only be added once it's in beta. - … - object: A type that represents links to other objects. - `__typename` 'ObjectLinkValue', required: Discriminator value: ObjectLinkValue - `value` union: A union representing items that can be linked to. If you have a type that can be linked to, it can only be added once it's in beta. - object: AaSequence variant - … - object: Attachment variant - … - object: Box variant - … - object: Container variant - … - object: CustomEntity variant - … - object: DnaOligo variant - … - object: DnaSequence variant - … - object: DropdownOption variant - … - object: Entry variant - … - object: Inaccessible variant - … - object: Location variant - … - object: MatrixPlate variant - … - object: Mixture variant - … - object: Molecule variant - … - object: OligoConjugate variant - … - object: OligoDuplex variant - … - object: Protein variant - … - object: Result variant - … - object: RnaOligo variant - … - object: RnaSequence variant - … - object: Run variant - … - object: WellPlate variant - … - object: A type that represents text (string) values with an associated URL. - `__typename` string, required - `url` string: The URL associated with the value. Please use `TextValue` if you don't want a URL. - `value` string: The text value. It may or may not be an empty string. - object: A type that represents text (string) values. - `__typename` string, required - `value` string: The text value. It may or may not be an empty string. ## Other responses - `400`: Bad Request - `403`: Forbidden - `404`: Not Found - `409`: Conflict - `429`: Too Many Requests - `500`: Internal Server Error --- [API](https://skmtc.dev/benchling/apis/benchling-api.md) - [All operations](https://skmtc.dev/benchling/apis/benchling-api/llms.txt) - [OpenAPI document](https://skmtc.dev/benchling/apis/benchling-api/revisions/c9f087b98b8b?raw)