Translational Research Informatics Software System
Medications
Family History
Questionnaires
Demographics
Visits History
Pathology
Storage Location
Gene Expression
Proteomic...
Patient Data Capture:
•Clinical & demographics info
•Patient’s specimens & derivatives
•Phenotypes & genotypes tracking
•A...
Specimen Data Capture:
•Physical measurements & desc.
•Current status & condition
•Storage location & barcodes
•Workflow p...
Calculate aliquots:
•by volume
•by mass
•by concentration
•by # of slides
Print barcodes:
•existing labels
•new GUID label...
- Design flexible specimen storage containers
- Batch assign & update samples to storage locations
- Generate or print fre...
Track specimens and
their derivatives’
lineage relationship
Associate image files
and all other types of
flexible, custom-...
Multiple data record updates
You can update
multiple sample
records:
…via Labmatrix’s
graphic user
interface…
… or through...
Proprietary & Confidential
Define shortcuts to quickly
create all expected sample
records (and their derivatives)
based on...
•Create specimen requests
•Change & monitor approval status
•Check & resolve “pull-list” items
•Update & track shipment st...
Create any data form - tailored to your research
This is a scalable solution that
communicates with all data sources
Database
ETL
Framework
SOAP
tab-delimited
text
Data
Tr...
Now that you have:
•Collected… ()
•Standardized… (Not yet? Use built-in data cleaning tools)
•Normalized… (Not yet? Use b...
14
ExplorationAcquisition AnalysisAnalysis
Typical Scientific Data Workflow
1. Data Acquisition
• Excel, Access, homebrews...
Cryptic DB you’ll never
have easy access to
Case Study: Common Problem in Translational Research
The Solution Qiagram: our award-winning “draw-your-question”
interface - SQL or programming training NOT required!
Just dr...
Qiagram: a visual data query tool
Example 1: “reporting & operational statistics” data query
Qiagram: a visual data query tool
Example 2: hypothesis-driven data exploration
Centralize Data: web-accessible system enables multi-site collaboration and
data collection, data/site management, data QA...
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Labmatrix

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Labmatrix

  1. 1. Translational Research Informatics Software System
  2. 2. Medications Family History Questionnaires Demographics Visits History Pathology Storage Location Gene Expression Proteomics Custody History Track all clinical & research data in a hierarchical and relational manner that facilitates secure collaborative data entry, and easy ad hoc data retrieval. Etc… Etc… Patient Data Biospecimen Data The Patient and Biospecimen data hubs in Labmatrix
  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. Calculate aliquots: •by volume •by mass •by concentration •by # of slides Print barcodes: •existing labels •new GUID labels Research BioBank 1B Pathology Sample A597 (text-only label) Specimen Barcoding & Aliquoting
  6. 6. - Design flexible specimen storage containers - Batch assign & update samples to storage locations - Generate or print freezer maps & barcode labels Specimen Storage Management (electronic sample inventories) Freezer Map
  7. 7. Track specimens and their derivatives’ lineage relationship Associate image files and all other types of flexible, custom-defined data for specimens Track Lineage, Images, and Custom-Defined Data
  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. Proprietary & Confidential Define shortcuts to quickly create all expected sample records (and their derivatives) based on your study’s specific SOPs or workflows “Specimen Factory”: one-click to generate all samples in your workflow
  10. 10. •Create specimen requests •Change & monitor approval status •Check & resolve “pull-list” items •Update & track shipment status Manage sample requests, inventory resolution, and shipments
  11. 11. Create any data form - tailored to your research
  12. 12. This is a scalable solution that communicates with all data sources Database ETL Framework SOAP tab-delimited text Data Transformer Labmatrix Core API Custom Web Services DB SOAP Enterprise System RMI APIRMI Enterprise System WEB UIHTTP DB Large Flat Files DB SQL Scripts Web Forms, Data Files XML Java Objects .TXT Federation Engine DB DB Many ways to get data into the system: Labmatrix Framework
  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 best make use of them?
  14. 14. 14 ExplorationAcquisition AnalysisAnalysis Typical Scientific Data Workflow 1. Data Acquisition • Excel, Access, homebrews • (Electronic?!) forms, notes • LIMS & instruments output • Labmatrix forms & records • Other enterprise resources • Etc… 2. Data Exploration 3.Data Analysis • SAS, R • Spotfire • Tableau • Statisticians • Etc… • Easy, graphical queries • ETL & data cleaning tools • Formulas & calculations • Visualize charts & graphs
  15. 15. Cryptic DB you’ll never have easy access to Case Study: Common Problem in Translational Research
  16. 16. The Solution Qiagram: our award-winning “draw-your-question” interface - SQL or programming training NOT required! Just drag & drop, and run your query!
  17. 17. Qiagram: a visual data query tool Example 1: “reporting & operational statistics” data query
  18. 18. Qiagram: a visual data query tool Example 2: hypothesis-driven data exploration
  19. 19. Centralize Data: web-accessible system enables multi-site collaboration and data collection, data/site management, data QA/review/reports, and immediate data querying results; scalable, web browser client-server architecture Encourage Standardization: increase & mandate data quality via standardized (and customizable) data-entry interfaces, standardized vocabularies, and standardized data models Enforce User Roles & Permissions: flexible configurations of how different users/groups/TAs can access specific data sets in collaborative settings Maintain Security & Compliance: transmit data securely, facilitate regulatory compliance, and track all data changes via detailed audit logs in this HIPAA/PHI-compliant system; customizable data backup & recovery plans Integration & Interoperability: multiple interfaces to communicate with other data systems in your IT infrastructure; vocabulary & ontology definitions KEY FRAMEWORK FEATURES

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