Bulk Registration of Entities: /Documentation/Archive/20.7

Bulk Registration of Entities

Many entity types can be uploaded in bulk using any common tabular format. Protein and nucleotide sequences can be imported using the GenBank format.

Upon upload, the registry will calculate and create any molecular species and sets as appropriate.

Assemble Bulk Entity Data
Bulk Upload Entity Data
Bulk Data Examples

You can bulk upload the following entity types:

Cell Lines
Molecules
Nucleotide Sequences
Protein Sequences
Vectors
Constructs
Expression Systems

And the following other types:

Mixtures
Mixture Batches

Supported File Formats

Tabular file formats are supported for all entity types:

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

Nucleotide sequences, protein sequences and constructs can also be imported using GenBank file formats:

GenBank: .genbank, .gb, .gbk

LabKey Biologics parses GenBank files for sequences and associated annotation features. When importing GenBank files, corresponding entities, such as new nucleotide and protein sequences, are added to the registry.

Assemble Bulk Entity Data

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

To acquire a template Excel file for a given entity, do the following:

In the registry, go the entry type you with to upload.
Select Manage Entity > Import Data.

Click the Template button to download the template Excel file.

Open the Excel file, and add data as appropriate under the column headers. See examples below.

Bulk Upload Entity Data

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

Go the entity type you wish to import.
Select Manage Entity > Import Data.
On the Import page, either Upload Files or Copy-and-Paste Data using the tabs.

If you stay on the Upload Files tab, drag and drop your file into the target area and click Submit.

If you select the Copy-and-paste Data tab, select TSV or CSV as appropriate, copy and paste your data into the text box, and click Submit.

Bulk Data Examples

Example Nucleotide Sequence File

Notes:

Annotations: Add annotation data using a JSON snippet, format is shown below.

name	alias	description	flag	protSequences	sequence	annotations
NS-23	Signal Peptide 1	An important sequence.	FALSE	[{name: "PS-23"}]	CCCCTCCTTG GAGGCGCGCA ATCATACAAC CGGGCACATG ATGCGTACGC CCGTCCAGTA CGCCCACCTC CGCGGGCCCG GTCCGAGAGC TGGAAGGGCA	[ { name:"First Annotation", category:"Feature", type:"Leader", start:1, end:20 }, { name:"Another Annotation", category:"Feature", type:"Constant", start:30, end:50 } ]

When importing the rows for NucSequence, you can reference the corresponding ProtSequence and the translation start, end, and offset. (The offsets are 1-based.) An example:

name	alias	description	flag	protSequences	sequence	annotations
NS-100	Signal Peptide 1	some description	FALSE	[{name: "PS-100", nucleotideStart=1, nucleotideEnd=30, translationFrame=2}]	ATGGAGTTGGGACTGAGCTGGATTTTCCTTTTGGCTATTTTAAAAGGTGTCCAGTGT

Example Protein Sequence File

Notes:

Organisms: A comma separated list of applicable organisms. The list, even if it has only one member, must be framed by square brackets. Examples: [human] OR [human, rat, mouse]
?: The column header for the extinction coefficient (ε).
%?: The column header for the % extinction coefficient (%ε).

Name	Alias	Description	Nuc Sequences	Chain Format	Avg. Mass	pI	?	%?	Num. S-S	Num. Cys	Organisms	Sequence
PStest-150		Test sequence for import		1	13999.64	8.030	35500	2.54	1	2	[mouse, rat]	EVQLVESGEL IVISLIVESS PSSLSGGLVQ GGGSLRLSCA ASGELIVISL IVESSPSSLS YSFTGHWMNW VRQAPGKGLE WVGIMIHPSD SETRYNQKFK DELIVISLIV ESSPSSLSIR FTISVDKSKN TLYLQMNSLR AEDTAVYYCA RIGIYFYGTT YFDYIWGQGT

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	uknown	unknown
Potassium chloride	unknown	unknown

Downloadable Example Files

Download a sample file for a given entity type:

LabKey Support

LabKey Support