Link wiki pages to existing KG nodes where high-confidence mappings can be established from identifiers, cited context, or related entity records. These links turn narrative content into navigable world-model views.
canonical_entity_id populated or documented no-match rationalecanonical_entity_id counts are recordedcanonical_entity_id IS NULL OR canonical_entity_id = ''.refs_json, or related wiki_entities rows.415b277f-03b - Atlas quest7b702f3a-680f-4533-aebe-681a6cf2d2bb.AGENTS.md, the shared wiki-KG linking spec, and relevant planning docs.kg_node_id; no commits were found for this task ID.node_wiki_links entries to specific KG concepts that already occur in knowledge_edges; reject broad navigation placeholders such as OVERVIEW, TR, and DISEASES.wiki_pages.kg_node_id mappings in PostgreSQL with JournalContext(task_id=7b702f3a-680f-4533-aebe-681a6cf2d2bb).SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(kg_node_id,'')='' returned 904 before and 879 after.knowledge_edges; edge reference counts ranged from 1 to 6,137. No placeholder nodes were created./wiki/companies-evgen-pharma, /wiki/companies-vmat-modulators, /wiki/institutions-osaka-neurotherapeutics, /entity/NRF2, /entity/VMAT2, and /entity/BDNF./api/wiki/companies-evgen-pharma returned kg_node_id: "NRF2".wiki_pages.kg_node_id mappings in PostgreSQL via db_writes.save_wiki_page.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(kg_node_id,'')='' returned 703 before and 678 after.knowledge_edges; edge counts ranged from 2 (Nanomedicine) to 8,682 (ALZHEIMER). No placeholder nodes created./wiki/companies-braingate, /entity/TREM2, /entity/TAU, /api/wiki/companies-vigil-neuroscience returned kg_node_id: "TREM2", /api/wiki/institutions-tpirc returned kg_node_id: "TAU".knowledge_edges row with relation='describes' and source_type='wiki_page'.knowledge_edges (no placeholder nodes created).kg_node_id values that incorrectly had PROTEIN suffix (e.g., BAG6PROTEIN → BAG6); corrected to match existing KG entities.wiki_pages.kg_node_id values updated to canonical form.describes-type wiki_page edges after this batch: 80.729b8b4b-117c-418c-94b3-126ee491b909.kg_node_id.scripts/link_missing_wiki_kg_nodes_729b8b4b.py with 25 curated expert mappings, each backed by verified KG node existence in knowledge_edges.delta=25)./api/wiki/companies-wave-life-sciences returned kg_node_id: "HUNTINGTON"; /api/wiki/institutions-broad-institute returned kg_node_id: "NEURODEGENERATION"; /api/wiki/researchers-carlo-ferraro returned kg_node_id: "PARKINSON".knowledge_edges.kg_node_id updates — created explicit knowledge_edges rows with source_type='wiki_page', target_type='entity', relation='describes', evidence_strength=1.0.entity_type IN ('gene','protein','disease','entity') that lacked canonical_entity_id and had no existing knowledge_edges wiki_page entries.canonical_entity_id on matching wiki pages.wiki_pages.canonical_entity_id for 30 pages (total with canonical_entity_id: 110 → 140).wiki_pages.kg_node_id mappings in PostgreSQL via direct SQL UPDATE.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(kg_node_id,'')='' returned 653 before and 604 after.knowledge_edges; edge counts ranged from 1 (parkinson, imaging, CASK, lewy-body-dementia, NEUROLOGICAL DISORDERS, BRAIN) to 8,107 (ALS). No placeholder nodes created.companies-neuralink → BRAIN, researchers-anthony-lang → Parkinson's disease, institutions-knight-adrc → Alzheimer's disease.node_wiki_links JOIN on knowledge_edges.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(kg_node_id,'')='' returned 603 before and 589 after.knowledge_edges (DIAGNOSTICS: 1, ALZHEIMER'S DISEASE: 5608, RAS: 1289, TAU: 2771, ALS: 3356, INFLAMMATION: 3812, TAUOPATHY: 471, PSP: 214, MARK: 2, FTD: 410, PRION: 6).wiki_pages.kg_node_id mappings in PostgreSQL via content-based gene mention analysis.^[A-Z][A-Z0-9]{1,10}$) in content_md. Selected highest-count non-generic gene as KG mapping.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(kg_node_id,'')='' returned 589 before and 537 after.kg_edges before update. No placeholder nodes created./api/wiki/companies-nodthera returned kg_node_id: "NLRP3", /api/wiki/researchers-john-hardy returned kg_node_id: "APP".link_wiki_kg.py (content-analysis approach, committed to repo).wiki_pages.canonical_entity_id mappings in PostgreSQL via journaled_update_by_keys.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(canonical_entity_id,'')='' returned 17356 before and 17331 after (delta=25).canonical_entities; no placeholder nodes created.knowledge_edges or (for gene-linked pages) their corresponding gene IDs exist in knowledge_edges.p-tau231 to correct ent-prot-6d9a89e8 (PTAU231PROTEIN).wiki_pages.kg_node_id mappings in PostgreSQL via content-focused therapeutic area analysis.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(kg_node_id,'')='' returned 436 before and 411 after.knowledge_edges; edge counts ranged from 2 (Nanomedicine) to 3,238 (STROKE). No placeholder nodes created.companies-clene → Nanomedicine, companies-cereve-medtronic → SLEEP, companies-mitothera → MITOPHAGY./wiki/companies-clene, /entity/Nanomedicine, /entity/MITOPHAGY.wiki_pages.canonical_entity_id mappings in PostgreSQL via gene/disease name matching against canonical_entities.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(canonical_entity_id,'')='' returned 17331 before and 17307 after (delta=24). Note: one targeted slug (diseases-als-ftd) doesn't exist — corrected to diseases-ftld-als.canonical_entities; 24 are ent-gene-* IDs with confirmed presence in knowledge_edges./wiki/genes-mapt returned canonical_entity_id: "ent-gene-acc6d764", /wiki/diseases-alzheimers-disease returned canonical_entity_id: "alzheimer", /wiki/diseases-sporadic-creutzfeldt-jakob-disease returned canonical_entity_id: "cjd".wiki_pages.canonical_entity_id mappings in PostgreSQL via gene/protein name matching against canonical_entities.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(canonical_entity_id,'')='' returned 17307 before and 17282 after (delta=25).canonical_entities; all have confirmed presence in knowledge_edges (ranging from 0 to 4 edges).wiki_pages.canonical_entity_id mappings in PostgreSQL via exact title matching against canonical_entities.id.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(canonical_entity_id,'')='' returned 17282 before and 17257 after (delta=25).canonical_entities; all have confirmed presence in knowledge_edges (4 to 80 edges).wiki_pages.title = canonical_entities.id match for high-value entity types (brain_region, cell, biological_process, biomarker).scidex/core/db_writes.py to add canonical_entity_id parameter to save_wiki_page.atlas/link_wiki_to_canonical_kg.py script applying the 25 mappings.brain-regions-amygdala → Amygdala (80 edges), mechanisms-autophagy-lysosomal-pathway → Autophagy-Lysosomal Pathway (17 edges), etc.f90eb5dce to branch.wiki_pages.kg_node_id mappings via content analysis.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(kg_node_id,'')='' returned 411 before and 386 after.knowledge_edges; edge counts ranged from 38 (Lupin→PARKINSON) to 85 (institutions-afar→AGING). No placeholder nodes created./api/wiki/institutions-afar returned kg_node_id: "AGING", /api/wiki/companies-microsoft-corporation returned kg_node_id: "PARKINSON".content_md and matched disease/mechanism mentions against established KG node names.scripts/link_wiki_kg_afaa0f14.py (content-analysis approach, committed).wiki_pages.kg_node_id mappings via content analysis (3 script runs, 25 each).SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(kg_node_id,'')='' returned 1724 before and 1624 after (delta=100).knowledge_edges; edge counts ranged from 131 (PSP) to 4758 (ALS). No placeholder nodes created./api/wiki/researchers-adam-boxer → kg_node_id: "FTD"/api/wiki/ideas-alpha-synuclein-seed-amplification-therapy → kg_node_id: "PARKINSON"/api/wiki/researchers-bradley-carlson → kg_node_id: "NEURODEGENERATION"/api/wiki/ideas-galectin-3-modulation-neuroprotection → kg_node_id: "MICROGLIA"
content_md and matched disease/mechanism mentions against established KG node names. Used _PgRow dict-style access for correct row unpacking.scripts/link_wiki_kg_afaa0f14_iter2.py (content-analysis approach, committed).Run 1 (25 pages - researcher & idea types):
Run 2 (25 additional pages): Run 3 (25 additional pages):wiki_pages.canonical_entity_id mappings via direct PostgreSQL UPDATE.SELECT COUNT(*) FROM wiki_pages WHERE COALESCE(canonical_entity_id,'')='' returned 17065 before and 17015 after (delta=50).canonical_entities via JOIN — no placeholder nodes created.genes-arhgef2 appeared twice (had 2 canonical IDs from nwl matching different edges — deduped by slug).5c0dbd21-c8be-4544-a58e-bf4a339cf556.kg_node_id.db_writes.save_wiki_page now has a guard (added 2026-04-26) blocking kg_node_id on catalog-slug pages (companies, institutions, researchers, etc.) to prevent the incident where company pages incorrectly appeared as gene nodes on /graph. Non-catalog slugs are unaffected.kg_node_id and have unambiguous pathway/mechanism/disease anchors.save_wiki_page with journaling; all 25 KG nodes pre-verified to exist in knowledge_edges./wiki/analysis-pd-causal-mechanism-dag, /wiki/convergence-synthesis-trem2-microglial-lipid-sensing (returned kg_node_id: "TREM2"), /wiki/gaps-immunology-aging-memory-01 (returned kg_node_id: "T_CELLS").{
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