feat(kg): add markdown export format for knowledge graph
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- Add kg_ocr/export/markdown_exporter.py with export_markdown() - Cluster entity co-occurrences using Louvain community detection - Wire -f markdown into `ocr-pipeline kg export` CLI command with KG_REPORT.md default - Add unit and CLI tests in tests/test_graph.py - Document markdown export in README.md - Untrack pycache binaries and ignore graphify-out and KG_REPORT.md
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@@ -79,6 +79,7 @@ uv run ocr-pipeline kg query data/ocr_output/kg_graph.json --entity BRCA1 --expa
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uv run ocr-pipeline kg query data/ocr_output/kg_graph.json --citation 10.1038/nature12345
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# export
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uv run ocr-pipeline kg export data/ocr_output/kg_graph.json -f markdown
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uv run ocr-pipeline kg export data/ocr_output/kg_graph.json -f graphml
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uv run ocr-pipeline kg export data/ocr_output/kg_graph.json -f neo4j
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```
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@@ -239,4 +240,3 @@ Gene/protein names go through scispaCy's `en_core_sci_lg`. Chemical formulas
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and units (µM, ng/mL, kb/Mb/Gb, °C, ×g) get normalized, scientific notation
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gets cleaned up (`1.5×10⁻³` → `1.5×10^-3`), and gel/blot figures get their
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captions pulled out separately.
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