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:
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:
Related Topics
