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GSK: How Knowledge Graphs Improve Clinical Reporting Workflows
This document discusses GSK's efforts to use knowledge graphs to improve clinical reporting workflows. It describes GSK's current multi-step clinical data flow process and the resources required. The document envisions a future where a clinical knowledge graph could provide a single connected data model, parallel processing, and accelerated decision making. GSK plans to test building a minimum viable product knowledge graph to ingest and analyze clinical trial data and derive metrics. The goal is to demonstrate feasibility and inform further development through a phased agile approach.
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- 1. gsk.com How will knowledgegraphsimprove clinical reporting workflows? Presenters: Alexey Kuznetsov (alexey.k.kuznetsov@gsk.com) & Shannon Haughton(shannon.l.haughton@gsk.com) 16Nov2022
- 2. 21 March 20232 Our Problem Statement Tremendous Resource, Multiple Handoffs, Numerous Transformations Single Study SDTM* ADaM TFLs Submission 5 – 10 studies 99 modules *From 77 legacy datasets Clinical data flow Trial design Collect data Review observed datasets Analyse datasets Review results EDC Lab data Randomisation Others... Protocol Metadata Examples 71 datasets 42 datasets <= 250 outputs SDTM ADaM TFLs 350 - 710 to integrate 210 – 420 to integrate <= 250 integrated outputs Re-transformations (Several Standard) Re-Mappings (Several Standards)
- 3. 21 March 20233 Imagine a world where anything is possible… True automation of standard analyses Ad-hoc requests delivered on demand (Blinded) Analysis results reviewedin real-time Manual effort of results validation virtually eliminated Data visualisations available in-stream GDPR and patient consent Risk-based monitoring is proactive Google-like Q&A system for our trial data Clinical application of preclinical AI algorithms
- 4. 21 March 20234 From Imagination to Reality Clinical Knowledge Graph Let’s move away from isolated data domain silos… …to ONE contextualised Clinical Knowledge Graph Exposure Domain Subject = Bob Study Day = 1 Dosage = 40mg Trial = Trial1 MedicalHistory Domain Subject = Bob Event Date = 2000 Term = Hypertension Trial = Trial1 Adverse Events Domain Subject = Bob Study Day = 1 Term = Headache Trial = Trial 1 Demographics Domain Sex = M Age = 75 Subject = Bob Trial = Trial1 Clinical Knowledge Graph
- 5. 21 March 20235 Our Idea …the Google Translate for our clinical data – helping us translate our complex data landscape to answer important scientific questions Clinical data flow Trial design Collect data Review observed datasets Analyse datasets Review results EDC Lab data Randomisation Others... Protocol Metadata Examples 99 Modules GSK Design (1 Standard) One Connected Data Model Parallel Processing SDTM (71) ADaM (42) TFLs (<=250) ISS/ISE Select Required Standard ETL Modules Parallel Processing
- 6. 21 March 20236 Unique Value KnowledgeGraph Greater control over data privacy Modern graph analytics & visualisation Decoupling vertical data pipeline Accelerated decision making
- 7. 21 March 20237 Goal: Test feasibility, desirability & sustainability of idea Phased agile & risk-based approach with predefined success criteria EXPERIMENT 1 Can we ingest SDTM data into CLD MVP? EXPERIMENT 3 Can we analyse, report and egress TLFs from CLD MVP? EXPERIMENT 2 Can we enrich CLD MVP model with ADaM Transformations? 2021 H1 2021 H2 2022 H1 2022 H2 MVP PILOT Can we use the CLD MVP to perform QC for an ongoing trial? Continuouslearning and iteration
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- 29. 21 March 202329 Open source assets released To be released: • tab2neo • neo4cdisc GSK-Biostatistics/neointerface: NeoInterface -Neo4j made easy for Python programmers!(github.com) read/write csv, xls, xlsx, xpt, sas7bdat, rda dm/ae/lb/... dm/ae/../custom
- 30. 21 March 202330 Learnings that helped us accelerate our idea Pre-defined success criteria critical in quick decision making Prioritise 1 idea, test it, refine it, test it, refine it… Focused innovation challenge can greatly help test disruptive ideas Understand painpoints & test ideas to drive informed innovation Timeboxed focused sprints are great to inform the path ahead
- 31. 21 March 202331 Special thanks to… Jorine Putter Michael Rimler Samantha Warden Kirsten Langendorf Johannes Ulander Dave Iberson-Hurst Eleanor Sparling Rachel Ren James Sefton William McDermott Jonathan Deacon Benjamin Grinsted Julian West It takes a village to raise an idea…
- 32.