Integrating Clarity LIMS with Upstream Sample Accessioning Systems

This section discusses methods for integrating BaseSpace Clarity LIMS with upstream sample accessioning systems.

The following illustration shows a typical architectural overview:

Creating a Sample in Clarity LIMS

Required:

• A sample must have a Name / ID

• A sample must be associated with a Case / Patient / Study / Project

• A sample must be associated with a Container (Tube / Plate etc)

Optional (but expected):

User-defined fields (UDFs)/custom fields (defined by your LIMS configuration)

Typical flowchart of actions within the broker:

The following animation illustrates the elements of an XML sample-creation message to Clarity LIMS.

Common options for the broker

Build your own:

• Pro: Not too difficult

• Con: Stability as number of messages increases

• ?: Maintainable over the long-term

Use a commercial / open-source offering (e.g. Mirth Connect)

• Pro: Quicker than build

• Pro: Robust, multi-threaded support for millions of messages per day

• ?: May prove to be an excessive or over-complicated means to accomplish something relatively simple

Does the broker need to carry out other business logic?

For example, one customer added logic to their broker that dealt with medical billing and was able to distinguish between physicians ordering duplicate tests for a subject (not reimbursable, therefore the duplicate sample wasn’t submitted to Clarity LIMS), versus a temporal study that was reimbursable.

The best practice is to take advantage of as many legacy systems as possible, rather than creating samples in Clarity LIMS, then reinventing business logic to remove unwanted ones.