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docs: add plan for graph expansion and optimization#1

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docs/scale-knowledge-graph-plan-6869368970008525253
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docs: add plan for graph expansion and optimization#1
sandeepmanimala wants to merge 4 commits intomainfrom
docs/scale-knowledge-graph-plan-6869368970008525253

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This PR introduces a PLAN.md file that outlines a roadmap for expanding and scaling the Multi-Omics Knowledge Graph.

Based on discussions with the user, this plan details two main phases:

  1. Phase 1: Expanding Data & Dimensions
    • Integration of Epigenomics (DNA Methylation) to link genes to epigenetic states.
    • Integration of Metabolomics (HMDB) to map circulating metabolites to the microbiome and phenomics.
    • Integration of 3D Protein Structures (AlphaFold) to add structural context to existing proteins and pharmacological docking.
  2. Phase 2: Performance & Scale Optimizations
    • Implementation of Apache Spark (PySpark) to handle massive ETL processes required for new billion-row datasets.
    • Refactoring ingestion to utilize the native Neo4j Admin Import tool over transactional Cypher imports.
    • Database tuning, B-tree/vector indexing, and transitioning to a clustered Neo4j Enterprise architecture.

PR created automatically by Jules for task 6869368970008525253 started by @sandeepmanimala

Co-authored-by: sandeepmanimala <154022739+sandeepmanimala@users.noreply.github.com>
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google-labs-jules Bot and others added 3 commits March 12, 2026 15:07
…4j admin import pipelines

Co-authored-by: sandeepmanimala <154022739+sandeepmanimala@users.noreply.github.com>
Co-authored-by: sandeepmanimala <154022739+sandeepmanimala@users.noreply.github.com>
Co-authored-by: sandeepmanimala <154022739+sandeepmanimala@users.noreply.github.com>
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