This topic describes how to use the Biologics application to create new entities, i.e. members of any data class in the Bioregistry, including cell lines, molecules, nucleotide sequences, expression systems, etc. Users creating entities may specify a name, or have one generated for them using a naming pattern. Entity names can also be edited later. If desired, administrators may also hide the ability to specify or edit names.

Create Entities in the User Interface

In this example, we show creation of a new cell line. Other kinds of entities will have different fields that compose them, and may also have additional tabs in the creation wizard. See specific documentation listed at the end of this topic.

  • Provide the details in the registration wizard:
  • Name: Provide a short unique name, or leave this field blank to have one generated using the naming pattern for this data class.
    • Hover over the to see an example generated name.
  • Description: Optional, but will be shown in the grids and can be a helpful way to illustrate the entity.
  • Common Name: Every entity includes a field for the common name.
  • Remaining fields: Required fields are marked with an asterisk.
  • When the fields are completed, click Finish to create the new entity.

You can now return to the grid for this data class (i.e. Cell Lines in this example) to find your new entity later.

Create/Import Registry Entities from File

For bulk registration of many entities in Biologics, including registry data class members, samples, assay result data, ingredients, and raw materials, you can make use of importing new data from file. Templates are available to assist you in reliably uploading your data in the expected format.

Obtain Template

Obtain a template by opening the type of entity you want to create, then clicking Template.

You can also find the download template button on the overview grids for each Bioregistry data class, and the main Sample Types and Assay listings. If you wait until you are importing data from a file, you can also find the Template button in the import interface.

Use the downloaded template as a basis for your import file. It will include all possible columns and will exclude unnecessary ones. You may not need to populate every column of the template when you import data.

  • For example, for a Sample Type, if you have defined Parent aliases, all the possible columns will be included in the template, but only the ones you are using need to be included.
  • In cases of columns that cannot be edited directly (such as the Storage Status of a sample, which is defined by a sample having a location and not being checked out), these columns will be omitted from the template.
  • Note that the template for assay designs includes the results columns, but not the run or batch ones.

Import Data From File

For Bioregistry entities, Samples, Assays, and Ingredients and Raw Materials, you can select Add > Import from File to use the file import method of creation. Select the Registry Type and select or drag and drop the spreadsheet containing your data into the target area. Starting from the template makes file import easier.

Check the box if you wish to Update data for existing registries during this file import.

Learn more about updating registry entities during import in this topic:

Entity Naming Patterns

If you do not provide a name, the naming pattern for the data class will be used to generate one. Hover over the to see the naming pattern in a tooltip.

The default naming patterns in LabKey Biologics are:

EntityDefault Naming Pattern
Cell LinesCL-${genId}
CompoundsCMP-${genId}
ConstructsC-${genId}
Expression SystemsES-${genId}
Molecular SpeciesMSp-${genId}
Molecule SetsMS-${genId}
MoleculesM-${genId}
Nucleotide SequencesNS-${genId}
Protein SequencesPS-${genId}
VectorsV-${genId}

To change a naming pattern, edit the Data Class definition.

Hide Name Entry/Edit Options

An administrator can hide the Name field for insert, update, or both by using Query Metadata overrides on a data class basis.

  • When insert of names is hidden, they will be generated using the naming pattern for the data class.
  • When update of names is hidden, names remain static after entity creation.
For example, to hide the Name field for cell lines for both insert and update use the following:

<tables xmlns="http://labkey.org/data/xml">
<table tableName="CellLine" tableDbType="NOT_IN_DB">
<columns>
<column columnName="Name">
<shownInInsertView>false</shownInInsertView>
<shownInUpdateView>false</shownInUpdateView>
</column>
</columns>
</table>
</tables>

An administrator can also disallow user-defined names throughout the system as described in this topic:

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