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Incorporating 'Patient Data' to Knowledge Graphs

What the AI Co-Scientist Paper Actually Demonstrates for Biologists and Data Scientists

September 18, 2025
10:30 AM PST / 1:30 PM EST

Clinical and real-world datasets hold enormous potential for translational research, but their complexity makes them hard to use. A single patient record can span labs, imaging, omics, and outcomes-yet much of this information is fragmented, inconsistently defined, and difficult to unify. Most EHRs capture little more than demographics and diagnoses, leaving critical measurement data out of reach.

Polly KG solves this by seamlessly integrating molecular data with patient data records, transforming scattered datasets into a living, semantically rich knowledge graph. It combines curated proprietary knowledge with high-quality public sources, ensuring both coverage and scientific rigor. The system is immediately usable yet fully customizable, so teams can adapt scoring logic, ontologies, and cohort definitions to their needs.

Unlike rigid platforms, Polly KG keeps raw data structured while surfacing analysis-ready features-like biomarker associations, outcomes, and differential expression-that can be queried in plain English. With built-in provenance and confidence scores, it helps organizations accelerate discovery, design smarter cohorts, and reach trial readiness in months, not years.

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Meet the Expert of this discussion
Krutika Gaonkar
Senior Manager, Partnerships, Elucidata

Real-World Applications We’ll Cover

  • Scaling clinico-genomic data integration: Large pharmaceutical organizations working with external data providers used Polly to build interoperable clinico-genomic data products 6x faster.
    Although purchased datasets are often labeled as "clean," they still lack interoperability—Polly's pipelines bridge this gap with robust integration and harmonization.

  • Information Retrieval: Drug safety monitoring teams used Polly's Knowledge Graph powered co-scientist to conversationally retrieve the right cohorts & assess drug response—cutting discovery time by 70%.

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Join us for a behind-the-scenes look at a Multi-agent AI system that achieves:
  • 93% recall across 23 key metadata fields including tissue, disease, cell line, donor ID, and treatment.
  • Outperformance of GPT-4.1 single-pass prompting on accuracy, F1 score, and traceability.
  • Curation of 4652 samples from 78 GEO datasets in days instead of weeks.
  • 4x reduction in manual effort equivalent to replacing a 3-person expert team working for 1 month.
  • Human-level accuracy, with 100% concordance on disease and 97% on gender based on CellxGene benchmarks.
  • Traceable records with field-level evidence attribution and confidence scores.
Register for our webinar to see how the Agentic AI system fits into scalable data workflows.

What You’ll Learn

  • Ask better questions, faster: Use natural language to query multimodal datasets - including patient data records and multi-omics - without needing data engineering support.
  • Unify 20+ data sources into one system: See how Polly KG connects structured and unstructured data - from single-cell and GWAS to experiment logs, clinical trials, and EHR into a single evolving graph.
  • Customize to scale: Tailor scoring logic, ontologies, cohort definitions, and access controls. Customization isn’t optional, it’s what makes AI usable in science.
  • Stay grounded in science: Polly KG blends expert-curated knowledge with interpretable AI, bridging the gap between algorithmic output and scientific reasoning.
  • Live Demo: Watch Polly KG in action: from querying in plain English to exploring scored results across multimodal and clinical datasets.

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Meet the Expert of this discussion
Krutika Gaonkar
Senior Manager, Partnerships, Elucidata
Meet the Expert of this discussion
Krutika Gaonkar
Senior Manager, Partnerships, Elucidata
What Sets polly KG Apart
Natural language querying with reasoning on
the roadmap
Cross-species graphs built from both proprietary
and public data
Custom scoring logic and domain-specific
ontology support
Seamless integration with internal tools, platforms,
and security frameworks
Who Should Attend
Translational Scientists and Discovery Leads
Computational Biologists and Data Scientists
Platform Owners, heads of R&D IT
Innovation and AI Strategy Teams
Who Should Attend
Translational Scientists and Discovery Leads
Data Science & Informatics Teams
Computational Biologists and R&D IT Leaders
Innovation & AI Strategy Teams

Why This Matters for Biomedical Researchers

If you’re working with complex biological data, you may be asking:

  • Can generative AI truly assist in scientific reasoning, not just data analysis?

  • What does it mean for hypothesis generation, literature review, or even designing experiments?

  • Could this accelerate—not replace—my discovery pipeline?

Whether you're skeptical, curious, or already experimenting with AI in your lab—this is a session designed to ground your understanding in evidence, not speculation.

Traditional KG

Polly KG

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Meet the Expert of this discussion
Krutika Gaonkar
Senior Manager, Partnerships, Elucidata
Key Takeaways
How data providers ensure adherence to quality standards through validation and compliance.
How GUI-based workflows, CLI tools, and collaborative workspaces enable streamlined data ingestion and synchronization at scale.
Understand how automated pipelines assess conformance, plausibility, and consistency, ensuring high-quality, AI-ready data products.
Key Takeaways
Reduce operational costs by streamlining data delivery through reusable, governed products.
Accelerate diagnostic development and clinical trial execution by delivering compliant, high-quality data at scale.
Improve audit readiness and regulatory confidence through governed data products and built-in quality assurance.
Equip cross-functional teams to act on trusted data—faster, and with greater confidence.
Who Should Attend
Translational Scientists and Discovery Leads
Computational Biologists and Data Scientists
Platform Owners, heads of R&D IT
Innovation and AI Strategy Teams
What Sets polly KG Apart
First KG to integrate molecular data alongside patient data records
Feature distillation pipeline for high-dimensional clinical and trial data
Base KG usable immediately, with flexible schema extensions
Cross-species graphs built from proprietary, public, and clinical datasets
Who Should Attend?

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