Translational Research Informatics Software System
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.
Patient Data Capture:•Clinical & demographics info•Patient’s specimens & derivatives•Phenotypes & genotypes tracking•All other customizable study data
Specimen Data Capture:•Physical measurements & desc.•Current status & condition•Storage location & barcodes•Workflow processing status•Usage & custody history
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
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
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)
“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
Create any data form - tailored to your research
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
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?
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
Case Study: Common Problem in Translational Research Cryptic DB you’ll never have easy access to
Qiagram: our award-winning “draw-your-question”The Solution interface - SQL or programming training NOT required! Just drag & drop, and run your query!
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/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