Integrating Clarity LIMS with Upstream Sample Accessioning Systems
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Clarity LIMS Software
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This section discusses methods for integrating BaseSpace Clarity LIMS with upstream sample accessioning systems.
The following illustration shows a typical architectural overview:
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.
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.
