This topic explains how to import Registry items in bulk using common tabular formats (Excel, TSV, etc) and GenBank or FASTA file formats.

• Assemble Bulk Entity Data
• Bulk Upload Entity Data

Supported File Formats

Tabular file formats are supported for all entity types:

• Excel: .xls, .xlsx
• Text: .csv, .tsv

Nucleotide sequences, protein sequences, constructs, and vectors can also be imported in bulk using sequence file formats:

• GenBank: .genbank, .gb, .gbk
• FASTA: .fasta, .fa, .fsa

LabKey Biologics parses these files for sequence data (GenBank files also carry associated annotation features), registering the corresponding entities in the Registry along with any relationships between them, such as a construct's insert sequences.

All the files included in a single import must be the same file type. You cannot combine GenBank and FASTA files, or either of these with a tabular file, in one import.

If the files you are importing add up to more than 100KB, the import runs as a background job instead of completing immediately, so you can continue working while it finishes.

Assemble Bulk Data

When assembling your entity data into a tabular format, keep in mind that each Registry Source Type has a different set of required column headings.

• Acquire a template Excel file for a given entity by clicking Template from the Registry Source Type overview page.
• Open the Excel file, and add data as appropriate under the column headers. See examples below.

Bulk Upload Registry Source Data

After you have assembled your information into a table, you can upload it to the registry:

If you want to update existing registry sources or merge updates and creation of new sources, use Edit > Update from File. This is supported for tabular files only; updating existing sequences via GenBank or FASTA import is not supported.

Bulk Data Example Files

The examples below form a coherent IgG1 antibody dataset. Import them in order — Nucleotide Sequences, Protein Sequences, Molecules, Constructs, Cell Lines, and finally the Expression System — and each file will find its referenced entities already in the Registry.

Example Nucleotide Sequence File

Notes:

• Prot Sequences: Provide PS names as a comma-separated list. To specify translation start, end, or frame, use JSON format (see NS-HC-001 below).
• Annotations: Add annotation data using a JSON snippet, as shown below.

name	alias	description	flag	protSequences-OPTIONAL	sequence	annotations
NS-LC-001	IgG1 Light Chain CDS	IgG1 light chain coding sequence	FALSE	PS-LC-001	ATGGACATCC AGATGACCCAG TCTCCATCCT CCCTGTCTGC ATCTGTAGGA GACAGA
NS-HC-001	IgG1 Heavy Chain CDS	IgG1 heavy chain coding sequence	FALSE	[{name: "PS-HC-001", nucleotideStart:1, nucleotideEnd:57, translationFrame:1}]	ATGGAGTTGG GACTGAGCTG GATTTTCCTT TTGGCTATTT TAAAAGGTGT CCAGTGT	[{"name":"CDR1","category":"Feature","type":"CDR","start":1,"end":24},{"name":"Framework","category":"Feature","type":"Framework","start":25,"end":57}]

Example Protein Sequence File

Notes:

• Nuc Sequences: A comma-separated list of nucleotide sequence names. To specify translation start, end, or frame, use JSON format.
• Organisms: A comma-separated list. Examples: human or human, rat, mouse.

Name	Alias	Description	Nuc Sequences	Chain Format	pI	Num. S-S	Num. Cys	Organisms	Sequence
PS-HC-001	IgG1 HC	IgG1 heavy chain protein	NS-HC-001	1	8.23	4	6	human	EVQLVESGEL IVISLIVESS PSSLSGGLVQ GGGSLRLSCA ASGELIVISL IVESSPSSLS YSFTGHWMNW VRQAPGKGLE WVGIMIHPSD SETRYNQKFK DELIVISLIV ESSPSSLSIR FTISVDKSKN TLYLQMNSLR AEDTAVYYCA RIGIYFYGTT YFDYIWGQGT
PS-LC-001	IgG1 LC	IgG1 light chain protein	NS-LC-001	2	6.75	2	3	human	DIQMTQSPSS LSASVGDRVT ITCSASQDIS NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQQ YDNLWTFGGG TKVEIK

Example Molecule File

You can import molecules and their components — Protein Sequences (PS), Nucleotide Sequences (NS), Compounds, and other Molecules — together from a single file. For each component, add a set of columns using the pattern Component-N/Field, where N is the component number (1, 2, 3, …).

Column	Description
Component-N/Name	Name of the component. Leave blank to have the system assign a name automatically.
Component-N/Type	Entity type: protsequence, nucsequence, compound, or molecule
Component-N/Sequence	The amino acid or nucleotide sequence, if you're creating a new PS or NS in the same file
Component-N/Description	Optional description
Component-N/Alias	Optional alias
Component-N/commonName	Optional common name
Component-N/Stoichiometry	Number of copies (optional)

How components are handled:

• If a component doesn't exist yet, it will be created automatically.
• If a component already exists, it will be linked to the molecule. Any other details for it in the file are ignored — linking doesn't update the existing component.
• You cannot create a Molecule as a component within the same file. Protein Sequences, Nucleotide Sequences, and Compounds can be created this way.
• Annotation data for components can be added through the Registry UI after import, or included in the file using JSON format (see the Nucleotide Sequence example above).

Templates: Template files for Molecules, Protein Sequences, and Nucleotide Sequences are available to download from the import page. The Molecule template comes with columns for two components — enough for a typical two-chain molecule.

TSV quoting: If a value contains a comma, wrap it in double quotes (for example: "PS-1, variant A").

Success page: After a successful import, the confirmation page lists all entities created, including any PS or NS components generated during the Molecule import.

Name	Description	Component-1/Name	Component-1/Type	Component-1/Sequence	Component-1/Stoichiometry	Component-2/Name	Component-2/Type	Component-2/Sequence	Component-2/Stoichiometry
MOL-001	IgG1 antibody (links existing chains)	PS-HC-001	protsequence		2	PS-LC-001	protsequence		2
MOL-002	IgG1 antibody variant (inline sequences)		protsequence	EVQLVESGEL	2		protsequence	DIQMTQSPSS	2

In the first row, existing protein sequences PS-HC-001 and PS-LC-001 are linked to the new molecule by name. In the second row, Component-1/Name and Component-2/Name are blank — new PS components are created with system-assigned names and the sequences provided inline.

Example Construct File

Notes:

• CompleteSeqID: The name of the Nucleotide Sequence that represents the full construct sequence.
• InsertSequences: A comma-separated list of Nucleotide Sequence names for the insert regions.

Name	Description	CompleteSeqID	InsertSequences
CONSTR-001	IgG1 expression construct	NS-HC-001	NS-HC-001, NS-LC-001

Example Cell Line File

Notes:

• Organisms: A comma-separated list. Examples: human, mouse, rat.
• stable: TRUE if the cell line is a stable transfectant.
• clonal: TRUE if the cell line is clonally derived.

Name	Description	Alias	commonName	stable	clonal	Organisms
CL-CHO-K1	CHO-K1 host cell line for IgG1 production	CHO-K1	Chinese hamster ovary K1	TRUE	TRUE	human

Example Expression System File

Notes:

• Constructs: A comma-separated list of Construct names.
• HostCellLineId: The name of the Cell Line used for expression.

Name	Description	Constructs	HostCellLineId
ES-001	CHO-K1 expression system	CONSTR-001	CL-CHO-K1

Mixtures and Batches

The text 'unknown' can entered for certain fields. For Mixtures, the Amount field; for Mixture Batches, the Amount and the RawMaterial fields.

Mixture Bulk Upload

Type	Ingredient/Mixture	Amount Unit Type
Ingredient	I-2	unknown

Batch Bulk Upload

Ingredient	Amount Used	Raw Material Used
Sodium phosphate dibasic anhydrous	5	RawMat-1234
Sodium Chloride	unknown	unknown
Potassium chloride	unknown	unknown

Related Topics

• GenBank Format
• Create Entity via File Upload