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
You can bulk upload the following entity types:
- Cell Lines
- Nucleotide Sequences
- Protein Sequences
- Expression Systems
And the following other types:
Supported File FormatsTabular 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.
- Click the dropdown triangle (located to the right of the Insert New button).
- Select 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:
Bulk Data Examples
Example Nucleotide Sequence File
- Annotations: Add annotation data using a JSON snippet, format is show below.
|NS-1001|| ||An important NS||A-1001||CCCCTCCTTG|
Example Protein Sequence File
- 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|
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
Batch Bulk Upload
|Type||Ingredient/Mixture||Amount Unit Type|
|Ingredient||Amount Used||Raw Material Used|
|Sodium phosphate dibasic anhydrous||5||RawMat-1234|
Downloadable Example Files
Download a sample file for a given entity type: