Translational Research Informatics Software System
The Patient and Biospecimen data hubs in Labmatrix   Demographics    Patient       Biospecimen          Pathology         ...
Patient Data Capture:•Clinical & demographics info•Patient’s specimens & derivatives•Phenotypes & genotypes tracking•All o...
Specimen Data Capture:•Physical measurements & desc.•Current status & condition•Storage location & barcodes•Workflow proce...
Specimen Barcoding & Aliquoting                                                      Research BioBank 1B                  ...
Specimen Storage Management (electronic sample inventories)          Freezer Map      - Design flexible specimen storage c...
Track Lineage, Images, and Custom-Defined DataTrack specimens andtheir derivatives’lineage relationship                   ...
Multiple data record updates                               You can update                               multiple sample   ...
“Specimen Factory”: one-click to generate all samples in your workflow    Define shortcuts to quickly    create all expect...
Manage sample requests, inventory resolution, and shipments                                     •Create specimen requests ...
Create any data form - tailored to your research
Many ways to get data into the system:                                              Large Flat             DB       DB  Th...
Now that you have:   •Collected… ()   •Standardized… (Not yet? Use built-in data cleaning tools)   •Normalized… (Not yet?...
Typical Scientific Data Workflow           Acquisition                    Exploration                 Analysis            ...
Case Study: Common Problem in Translational Research                                                       Cryptic DB you’...
Qiagram: our award-winning “draw-your-question”The Solution   interface - SQL or programming training NOT required!       ...
Qiagram: a visual data query toolExample 1: “reporting & operational statistics” data query
Qiagram: a visual data query toolExample 2: hypothesis-driven data exploration
KEY FRAMEWORK FEATURESCentralize Data: web-accessible system enables multi-site collaboration anddata collection, data/sit...
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Labmatrix Slides 2011 05

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Labmatrix Slides 2011 05

  1. 1. Translational Research Informatics Software System
  2. 2. The Patient and Biospecimen data hubs in Labmatrix Demographics Patient Biospecimen Pathology Data Data Medications Storage Location Family History Custody History Questionnaires Proteomics Visits History Gene Expression Etc… Etc…Track all clinical & research data in a hierarchical and relationalmanner that facilitates secure collaborative data entry, and easyad hoc data retrieval.
  3. 3. Patient Data Capture:•Clinical & demographics info•Patient’s specimens & derivatives•Phenotypes & genotypes tracking•All other customizable study data
  4. 4. Specimen Data Capture:•Physical measurements & desc.•Current status & condition•Storage location & barcodes•Workflow processing status•Usage & custody history
  5. 5. Specimen Barcoding & Aliquoting Research BioBank 1B Pathology Sample A597 (text-only label)Print barcodes:•existing labels•new GUID labels Calculate aliquots: •by volume •by mass •by concentration •by # of slides
  6. 6. Specimen Storage Management (electronic sample inventories) Freezer Map - Design flexible specimen storage containers - Batch assign & update samples to storage locations - Generate or print freezer maps & barcode labels
  7. 7. Track Lineage, Images, and Custom-Defined DataTrack specimens andtheir derivatives’lineage relationship Associate image files and all other types of flexible, custom-defined data for specimens
  8. 8. Multiple data record updates You can update multiple sample records: …via Labmatrix’s graphic user interface… … or through Excel and/or other text editors. (Also through our programmatic API)
  9. 9. “Specimen Factory”: one-click to generate all samples in your workflow Define shortcuts to quickly create all expected sample records (and their derivatives) based on your study’s specific SOPs or workflows Proprietary & Confidential
  10. 10. Manage sample requests, inventory resolution, and shipments •Create specimen requests •Change & monitor approval status•Check & resolve “pull-list” items•Update & track shipment status
  11. 11. Create any data form - tailored to your research
  12. 12. Many ways to get data into the system: Large Flat DB DB This is a scalable solution that Files DB Federation communicates with all data sources Engine SQL Scripts DB tab-delimited text Data SOAP ETL Transformer Framework Web Forms, Data Files Database HTTP WEB UI .TXT Labmatrix Core API Java Objects Enterprise RMI RMI API System DB Labmatrix XML Enterprise SOAP Custom Web Framework System Services
  13. 13. Now that you have: •Collected… () •Standardized… (Not yet? Use built-in data cleaning tools) •Normalized… (Not yet? Use built-in formula calculation tools)…some, or all of your project data, how do you bestmake use of them?
  14. 14. Typical Scientific Data Workflow Acquisition Exploration Analysis Analysis1. Data Acquisition 3.Data Analysis• Excel, Access, homebrews • SAS, R• (Electronic?!) forms, notes • Spotfire• LIMS & instruments output • Tableau• Labmatrix forms & records • Statisticians 2. Data Exploration• Other enterprise resources • Etc…• Etc… • Easy, graphical queries • ETL & data cleaning tools • Formulas & calculations • Visualize charts & graphs 14
  15. 15. Case Study: Common Problem in Translational Research Cryptic DB you’ll never have easy access to
  16. 16. Qiagram: our award-winning “draw-your-question”The Solution interface - SQL or programming training NOT required! Just drag & drop, and run your query!
  17. 17. Qiagram: a visual data query toolExample 1: “reporting & operational statistics” data query
  18. 18. Qiagram: a visual data query toolExample 2: hypothesis-driven data exploration
  19. 19. KEY FRAMEWORK FEATURESCentralize Data: web-accessible system enables multi-site collaboration anddata collection, data/site management, data QA/review/reports, and immediate dataquerying results; scalable, web browser client-server architectureEncourage Standardization: increase & mandate data quality viastandardized (and customizable) data-entry interfaces, standardized vocabularies, andstandardized data modelsEnforce User Roles & Permissions: flexible configurations of howdifferent users/groups/TAs can access specific data sets in collaborative settingsMaintain Security & Compliance: transmit data securely, facilitateregulatory compliance, and track all data changes via detailed audit logs in thisHIPAA/PHI-compliant system; customizable data backup & recovery plansIntegration & Interoperability: multiple interfaces to communicate withother data systems in your IT infrastructure; vocabulary & ontology definitions

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