Document Recognition (Extraction) Patterns (DRPs) are templates that include fields to parse from a document for a destination in other applications/databases. Elements such as keywords, tables, and graphs are identified and structured into UXML. This may be done manually by the user or automatically by the system and edited by the user. The Extraction Patterns tab allows you to delete already defined DRPs.
For detailed information about creating a template and defining a DRP during template configuration, refer to section Creating a Parsing Method (DRP). Briefly, when you create a template, you create a Data Recognition Pattern to isolate the keywords, table columns, and other required information in a document file. These identify the data that you want to use to update database tables in the LIMS. Next you map the keywords, table columns, graphs, and so on, to an Output XML template, so that data can be extracted from the document file and placed in a UXML structure. The UXML structure containing the extracted data is used later by a LIMS script to update LIMS database tables.
For example, you can create a DRP to parse results from an instrument file so the results can be used to update a LIMS RESULTS database table. You can upload an initial file into SDMS where you can familiarize yourself with the file contents. You can then assign keywords located in the file contents such as the Sample ID and results columns such as Analytes and Results that you know are used to update a LIMS RESULTS table. Then you can map those keywords to an output XML template to be used in transporting the data from the document to the LIMS.
After you complete this configuration and upload this type of document in the future, an UXML structure is generated and saved with the document. This UXML contains the values for the keywords, tables, images, and so on, in the document. To view an in-depth diagram of the process, see the section Designing Document Templates. The document with the attached UXML containing the structured data proceeds to the Export stage. The importing script for the document File Type is used to read the structured UXML and update the LIMS RESULTS table using the values from Sample ID, Analytes, and Results. For more information about assigning an import script to a file type, see the section File Types. After processing, the script performs a cleanup routine to release the document so it is not processed again, and the workflow is complete.
NOTE A STARLIMS service can be configured to run a batch application at intervals, such as every twenty minutes, to query SDMS for document files in the Export stage. The application runs the importing script with the UXML structure as an input parameter and this is how the extracted data is acquired to update STARLIMS tables.
The next section, Unified XML, helps you to create an output XML template.