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.

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.
  • 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:

  • Go the entity type you wish to import.
  • Click the dropdown triangle (located to the right of the Insert New button).
  • Select Import Data.
  • On the Import page, click either the Upload Files tab or the Copy-and-paste Data tab.
    • If you select the Upload Files tab, drag and drop your file into the target area and click Sumbit. (Or click the paperclip icon to browse to the file.)
    • If you select the Copy-and-paste Data tab, select TSV or CSV as appropriate, copy your data into your operating system's clipboard, paste it 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 show below.
NameFlagDescriptionAliasSequenceProt SequencesAnnotations
NS-1001 An important NSA-1001CCCCTCCTTG
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
}
]

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 ().
NameAliasDescriptionNuc SequencesChain FormatAvg. MasspI?%?Num. S-SNum. CysOrganismsSequence
PStest-150 Test sequence for import 113999.648.030355002.5412[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

TypeIngredient/MixtureAmount Unit Type
IngredientI-2unknown

Batch Bulk Upload

IngredientAmount UsedRaw Material Used
Sodium phosphate dibasic anhydrous5RawMat-1234
Sodium Chlorideuknownunknown
Potassium chlorideunknownunknown

Downloadable Example Files

Download a sample file for a given entity type:

Related Topics

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