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Domain-Agnostic Knowledge Graph Server

Stage 2: extraction

graphwright/kgraph

Domain-Agnostic Knowledge Graph Server

graphwright/kgraph

Home
Live tools
Live tools
Manifesto
Overview
Architecture
Identity
Identity
- Canonical IDs
- Deduplication
Trust
Trust
- Provenance
- Conflicting Claims
Ingestion
Ingestion
LLM Integration
LLM Integration
Schema
Schema
- Schema Design Guide
- Adapting to Your Domain
Storage and Export
Deployment and Operations
Examples
Examples
- Medlit
- Sherlock
Contributing
The Identity Server
The Identity Server
- Preface
- Part I: The Problem of Identity
  Part I: The Problem of Identity
- Part II: The Typed Graph
  Part II: The Typed Graph
- Part III: Integration
  Part III: Integration
- Part IV: Trustworthiness
  Part IV: Trustworthiness
- Appendix A: Identity Server Specification
  Appendix A: Identity Server Specification
- Appendix B: The Domain Spec Schema
- Appendix C: Reference Implementation Details
  Appendix C: Reference Implementation Details
Knowledge Graphs from Unstructured Text
Knowledge Graphs from Unstructured Text
- Preface
- Part I: The Landscape
  Part I: The Landscape
- Part II: LLMs Change the Equation
  Part II: LLMs Change the Equation
- Part III: Building It
  Part III: Building It
- Part IV: What It Makes Possible
  Part IV: What It Makes Possible
- Appendix A: Reference Implementation Notes
- Run all four stages over a named list of papers
- Stage 1: vocabulary
- Stage 2: extraction
- Stage 3: ingest (identity-server deduplication)
- Stage 4: build bundle
BFS-QL
BFS-QL
- Preface
- Part I: The Interface Problem
  Part I: The Interface Problem
- Part II: The Protocol
  Part II: The Protocol
- Returns only disease entities matching "breast cancer"
- Papers are excluded before ranking
  Papers are excluded before ranking
  - Overview
  - Chapter 7: MCP as the Delivery Mechanism
- Part III: Building a Backend
  Part III: Building a Backend
- Part IV: The Bigger Picture
  Part IV: The Bigger Picture
- Appendix A: BFS-QL Protocol Reference
Books

Stage 2: extraction¶

uv run python -m examples.medlit.scripts.extract \ --input-dir pmc_xmls --output-dir extracted \ --vocab-file vocab/vocab.json --papers PMC12345.xml,...

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