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Brewing SEDD In-House Automated generation and validation of Staged Electronic Data Deliverable in a commercial laboratory Jakub Rehacek, Ph.D., PEL Laboratories,

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Presentation on theme: "Brewing SEDD In-House Automated generation and validation of Staged Electronic Data Deliverable in a commercial laboratory Jakub Rehacek, Ph.D., PEL Laboratories,"— Presentation transcript:

1 Brewing SEDD In-House Automated generation and validation of Staged Electronic Data Deliverable in a commercial laboratory Jakub Rehacek, Ph.D., PEL Laboratories, Inc.

2 PEL Laboratories, Inc. Who are we? PEL Laboratories, Inc. is a small laboratory (50 people) Specializing in high end analytical and data management services Providing full service capabilities in Inorganic, Organic, and Wet Chemistry Analyses Highly automated

3 PEL Laboratories, Inc. Overview Laboratory Background Info SEDD Creation Prerequisites SEDD Generation SEDD Review and Validation

4 PEL Laboratories, Inc. Why is SEDD good for a Lab? PEL provides EDDs in over 100 different EDD flavors to its clients Parser maintenance issues Data exchange difficult – multiple contractors on the same project SEDD single common data format pass-thru review and validation by contractor

5 PEL Laboratories, Inc. Laboratory Background Data Acquisition LIMS QC Reports + EDDs Web Portal Web Services

6 PEL Laboratories, Inc. Data Acquisition Advanced stages of the SEDD deliverable call for high levels of detail in the reporting of analytical results. Success in automated SEDD generation starts at the bench. The data acquisition software must have the capability of providing complete access to the raw data underlying the acquisition of analytical results. PEL uses a suite of highly customized data acquisition software with automated transfer to LIMS.

7 PEL Laboratories, Inc. LIMS The success of automated SEDD generation actually starts long before the samples arrive at the laboratory Project Profile built during the bid phase QC and analytical requirements as well as HC and EDD format are locked in Real-time tracking and interaction with the Web Portal Automated QC review at each stage of lab processing McDonalds screen real-time project status All parameters required for SEDD are collected along the way and stored in LIMS

8 PEL Laboratories, Inc. Quality Control Automated batteries of Quality Control Checks at various stages of sample package generation Assembly-line, step-by-step, computer driven sample prep Barcode verifications of samples and spike solutions Reasons for manual integrations must be explained Sample Narratives are generated automatically Capture raw instrument data down to the chromatograms/spectrograms. All the data is kept in the system Cross-linked with clean-up/prep info and with calibration runs Essential ingredients for generation of the SEDD files.

9 PEL Laboratories, Inc. Reports EDD + Hard Copy Project Managers generate SEDD at the push of a button The SEDD is generated automatically in conjunction with hard copy reports directly from our LIMS. SEDD is validated as a part of the final package QC/data validation check sequence. We routinely generate both SEDD and customer-specified EDD at the same time in order to ease the transition into the SEDD-based deliverables. All information comes from the same source (LIMS) so that we can guarantee that the SEDD, custom EDD, and hardcopy will have identical values. We can re-generate SEDD deliverables for historical projects that have already been processed through the Lab, but reported in a different format.

10 PEL Laboratories, Inc. Web Portal Complete on-line data management system directly interfaced with LIMS Real-time Project Status/Package Tracking Preliminary results available online immediately after release Data Review and Validation Screening Criteria/Action Levels Chain-of-Custody Documents online Immediate Access to Test Results Executive Report" QC and calibration data is also available Hardcopy Reports available online Billing Information Historical billing information is maintained Automated project financial summaries to assist with the Sarbanes-Oxley Act disclosure Final invoices may be downloaded in PDF format Auto-Email Notification/Reports EDD's are available online at the same time the work order is finalized

11 PEL Laboratories, Inc. Web Services The next step in Client-Laboratory interaction A web service is a web site to be used by computer programs instead of by humans. Each web service is a small application accessible through the Internet. Web services use XML for transferring information. The SEDD deliverable is uniquely qualified for use as a data transfer medium between web services. Simple Excel spreadsheet transparently links to a laboratory web service to retrieve relevant analytical results for further processing.

12 PEL Laboratories, Inc. Automated Generation of SEDD Available Tools SEDD Tool – EPAs data converter Commercial LIMS Off-the-shelf tools (MS SQL Server,.NET)

13 PEL Laboratories, Inc. EPA SEDD Tool The SEDD Tool's primary task is to convert local database data into an Extensible Markup Language (XML)-compliant file for delivery to other remote data systems. The SEDD Tool addresses the U.S. Environmental Protection Agency's need to receive analytical data electronically from its contracting laboratories.

14 PEL Laboratories, Inc. Commercial LIMS Several commercial LIMS software vendors have incorporated the SEDD generation into their products. Laboratories have to work with the vendor to ensure that their SEDD generators are kept up to date with the latest changes in the SEDD format.

15 PEL Laboratories, Inc. Off-the-shelf tools The SEDD is an XML document. It can be created fairly easily with the use of generic programming tools. PEL chose the Microsoft product line because it links up with the business productivity software used in the lab. The MS SQL Server database platform provides a robust back-end foundation for data storage and manipulation. The Visual Studio.NET suite provides tools for development of data retrieval engines and user interfaces. Microsoft Office applications are the ultimate consumers of the final data products as they provide a familiar interface for users. All modern database and programming platforms have embraced the XML, and provide a multitude of tools to generate, manipulate, and consume the XML.

16 PEL Laboratories, Inc. Prerequisites for Automated SEDD generation All the fields must be available in LIMS Correct and streamlined back-end database structure. All the data elements required by SEDD must be present in the database. The correct linkages must be set. Required data are collected along the way as the samples are processed through the laboratory. The data acquisition is an integral part of the process, and can be streamlined. For example: the sample bottle ids are stored in the system the pre-weight information is also readily available for relevant calculations. pH and sample temperatures recorded Relationships established The SEDD file format stores the analytical results information as well as information about the relationship of the result to associated quality control samples and instrument calibration. These relationships must be established in the underlying data structures for error-free automated EDD generation.

17 PEL Laboratories, Inc. SEDD Generation Process Query LIMS – SQL The SEDD creation is a matter of querying the data store to retrieve the desired Work Order results and associated QC information. The amount of information and complexity of relationships between the SEDD nodes increases with each level of SEDD (1, 2a, 2b, 3). We have built a modular query and retrieval engine that brings in all relevant information based on the SEDD level being produced. XML export routine in.NET Visual Studio.NET provides a feature-rich environment for the creation of XML documents. Entire XML document is generated and fully formed according to the Document Type Definition (DTD) template. The System.XML namespace provides all classes necessary for creating, processing, and validation of XML files.

18 PEL Laboratories, Inc. Validation/Review Tool PELs Data Validation/Review tool is an on-line service that assists a project chemist or independent validator with review of our chemistry. Data review/Validation QC Reports

19 PEL Laboratories, Inc. Validate Review Chemistry The SEDD contains all necessary relationships between the results and QC samples validated against the DTD, and then parsed analytical runs are cross-referenced to prep batches and to calibrations reported results can be reviewed from many angles The SEDD Stage 3 allows clients to recalculate the results from the raw on-column values independently from our data processing software and LIMS.

20 PEL Laboratories, Inc. QC Review Reports Our Review tool makes it possible to generate reports quickly via our website. The reports include an Executive Summary report showing all values detected above the Method Detection Limit, and a comprehensive Laboratory Review Checklist (LRC) that quickly summarizes any exceptions. A detailed QC flagging report can also be created to assist with validation flag applications in our clients data systems. Our system can also export EDDs in multiple formats to facilitate transition from legacy data systems. Clients can upload the SEDD data file and export in ERPMS, ERIS, or any other format that PEL currently supports. PEL Laboratories, Inc., is currently working with other companies to facilitate automated communication in order to provide push-button validation of laboratory results.

21 PEL Laboratories, Inc. Questions Contact info: Jakub Rehacek, Ph.D. VP Information Systems PEL Laboratories, Inc. 813-247-2805

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