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This topic defines some common terminology used in LabKey Biologics LIMS. It also outlines the default Registry Source Types in the Biologics application, and their relationships to one another. You can access this information within the application by selecting Registry from the main menu, then clicking See entity relationships at the top of the page.

Definitions: "Registry Source" vs "Sample"

In LabKey Biologics LIMS, the terms "registry" and "samples" refer to different components or aspects of the system. The Registry is a database or collection of information about biologics entities, while Samples refer to the actual biological material or representations of it that are being managed within the system. The registry helps organize and provide context to the information about these entities, and samples are the tangible or digital representations linked to these entries in the registry.

Registry Sources:

  • "Registry" typically refers to a comprehensive database or collection of information related to biologics entities. This can include details about biologics, such as antibodies, cell lines, or other biological molecules, that are being studied or managed within the system. The registry serves as a centralized repository for metadata and information about these biological entities, "Registry Sources", often including details like names, identifiers, descriptions, origin, properties, and associated data.
  • "Samples" in LabKey Biologics usually refer to the physical or virtual representations of biological material that have been collected, stored, and are being managed within the system. Samples can include a variety of biological materials such as tissues, cell lines, fluids, or other substances. Each sample is typically associated with specific information, like collection date, source, location, processing history, and other relevant details. Samples are often linked to entries in the registry to provide a clear relationship between the biological entity and the actual physical or virtual sample associated with it.

Diagram of Registry Source Relationships

  • A Sequence is inserted into an empty
  • Vector to create a
  • Construct.
  • A host Cell Line and a Construct combine to form an
  • Expression System, which generates
  • Molecules.
  • Molecules are composed of:
    • Protein Sequences
    • Nucleotide Sequences
    • and/or other molecules.
  • Molecule Sets group together molecules with the same mature sequence.
  • Molecular Species are variants of molecules.


Composed of a mixture of protein sequences, nucleotide sequences, chemistry elements, and other molecules. Generally, "molecule" refers to the target entity.

Example Molecules
Molecule W = 1 (protein sequence A)
Molecule X = 1 (protein sequence B) + 2 (protein sequence C)
Molecule Y = 1 (nucleotide sequence D)
Molecule Z = 2 (nucleotide sequence E) + 2 (protein sequence F) + 2 (molecule W)

Molecule Set

The set of molecules that only differ from one another in terms of their leader sequences. See Vectors, Constructs, Cell Lines, and Expression Systems.

Molecular Species

After protein expression and other processes, all the entities that are detected for a particular molecule (different cleavage sites, post-translational modifications, genomic drift). See Vectors, Constructs, Cell Lines, and Expression Systems.

Protein Sequence

Single sequence comprised of amino acids (20 different amino acids).

Example Protein Sequences
protein sequence A = ACELKYHIKL CEEFGH
protein sequence B = HIKLMSTVWY EFGHILMNP

Nucleotide Sequence

A single sequence comprised of nucleic acids, can be either DNA (A, T, G, C) or RNA (A, U, G, C).

Example Nucleotide Sequences
nucleotide sequence A (DNA) = AGCTGCGTGG GCACTCACGCT
nucleotide sequence B (RNA) = AGCUGUUGCA GCUUACAUCGU

Along with being a component of a molecule, DNA sequences can be designed that encode for specific protein sequences when transferred into a cell line to create an expression system.


DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell. The most common type of vector is a plasmid - a long double-stranded section of DNA that has been joined at the ends to circularize it. In molecular biology, generally, these plasmids have stretches of DNA somewhere in their makeup that allow for antibiotic resistance of some sort, providing a mechanism for selecting for cells that have been successfully transfected with the vector.


A vector (generally a plasmid) that has had a stretch of DNA inserted into it. Generally, this DNA insertion encodes for a protein of interest that is to be expressed.

Cell Line

A host cell line is transfected with a Construct, bringing the new DNA into the machinery of the cell. These transfected cells (called an Expression System) are then processed to select for cells that have been successfully transfected and grown up, allowing for the production of cells that have the construct and are manufacturing the protein of interest. At times, these transfections are transient and all of the cells are used in the process. Other times, a new stable cell line (still a Cell Line) is produced that can continue to be used in the future.

Expression System

A combination of a Construct and a host cell

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