Analysis

Cross-cutting comparisons and syntheses across conditions, metals, and mechanisms. 47 articles in this category.

• Adversarial Audit — 2026 04 19
  5 publishable pages sampled (none had prior `audit_passed`). All audited as hostile reviewer per Rule 12.
• Author Outreach Campaign — Operational Plan
  Every paper in WikiBiome represents a relationship we have not yet opened. The ingestion step — reading the source carefully, summarizing it faithfully, cros...
• Auto Discovered Stubs — 2026 04 19
  Rule 13 scope discovery scan. Created 22 stub pages for terms with ≥3 source mentions and no existing page.
• Batch Preview — Auto Discovered Stubs 2026 04 19
  ```yaml title: Vanadium type: entity subtype: metal created: 2026 04 19 updated: 2026 04 19 sources: [] source_count: 0 tags: [transition metal, trace elemen...
• Batch Preview — Operational Analyses → Cureva
  Purpose: Per Rule 5 (batch preview before bulk transform), preview the diff on 3 representative dated operational analysis files before applying `platform: c...
• Batch Preview — Strip Bullet Leading Bold Labels Across Wiki/
  Karen reported: "Too many bolded texts are causing readability concerns, and it doesn't have that Wikipedia 'feel' for that reason." Measured scope (grep cou...
• Batch Preview — Stub Demotions 2026 04 19
  Previewing frontmatter changes for §2f source density demotion. 68 publishable pages are below threshold and need `stub: true` + `stub_reason`.
• Broken Wikilinks — 2026 04 16
  Total pages with broken links: 957
• Build Refusals — 2026 04 19
  These pages were excluded from the WikiBiome build because they are below their §2f source density threshold and are not marked `stub: true`. Per §2f, sub th...
• Categorize 2026 04 21 Autism Papers But Disorganized Not Yet Added Or Ingested
  Source: `raw/Autism papers, but disorganized. Not yet added or ingested` (now removed) Canonical: `raw/Autism spectrum disorder (ASD)` Method: Keyword based ...
• Cureva/WikiBiome Boundary Violations — 2026 04 18
  Pages scanned: All entities (~218), concepts (~173), analyses (~18) Total violations detected: 43 (across 18 pages) Fixed (mechanical rewrites): 8 pages, 9 s...
• Dedup 2026 04 21 Autism Papers But Disorganized Not Yet Added Or Ingested
  Canonical: `/Users/kmfp/Documents/Claude/Raw/raw/Autism spectrum disorder (ASD)` New: `/Users/kmfp/Documents/Claude/Raw/raw/Autism papers, but disorganized. ...
• Dietary Metal Exposure By Life Stage
  A synthesis of how dietary heavy metal exposure varies across the human lifespan, highlighting that the same metals present different risks at different deve...
• Dietary Metal Paradoxes: When Healthy Foods And Good Intentions Backfire
  This page identifies the contradictions and clinical dilemmas that become visible only when the 236 source pages in this wiki are read together. Each paradox...
• DOI Corrections — 2026 04 19
  The Link Health audit on 2026 04 19 flagged 222 sources where the stored DOI resolves, but to a paper different from the stored title. Karen's recurring comp...
• Ingest Completeness Audit — 2026 04 18
  Scope: Full audit of `/wiki/` against 6 completeness checks. Run date: 2026 04 18 Inventory: 1,706 source pages | 162 entities | 108 concepts | 41 signatures...
• Ingest Priority Queue — 2026 04 20
  Based on overnight resume 2026 04 19 order (darkness first) plus audit gap analysis.
• Ingest Resume — 2026 04 19
  Not yet committed — all new source pages are in working tree, uncommitted.
• Ingest Resume — 2026 04 20
  `08e3a047` — ingest: PMDD batch 4 — 3 new source pages
• Keystone Outreach — 2026 05 01
  | Bucket | Count | | | | | Total keystone sources in vault | 39 | | Karen authored (skip — author = Karen) | 3 | | External keystone sources | 36 | | Needs f...
• Link Health Audit — 2026 04 19
  Run mode: online
• Manual Review Items — 2026 04 18
  These source pages lack `evidence_level` and the body text didn't contain clear study design keywords. Manual review of the PDF is needed to assign the corre...
• Metal Disease Matrix: A Cross Source Synthesis
  This page synthesizes findings across 1,426 source pages to map the relationships between metals and disease. Where individual source pages document a single...
• Orphan Pages — 2026 04 16
  Pages with zero inbound wikilinks.
• Overnight Continuous Improvement Log — 2026 04 18
  Starting state: 1706 sources, 216 entities, 171 concepts, 41 signatures, 30 interventions, 8 STOPs, 16 analyses.
• Overnight Resume — 2026 04 18
  Cycles completed: 2 (Cycle 2 clean → exit) Total fixes applied: 985 Total deferred: 251 Commits: 1 (`db335ed3`)
• Resume File — 2026 04 21 Moderate Tier Page Creation
  Last session: Created 21 pages in the 20+ mention tier (critical + high priority). All complete. Next intended batch: Create pages for all terms with 10 19 v...
• Resume File — 2026 04 23 Food Heavy Metal Contamination Ingest
  Last completed: 2 Tier 1 source pages created (Sun 2025 DIGM/arsenic/bladder cancer, Davis 2020 salivary metals/oral microbiome). 8 Tier 2A source pages in p...
• Rule 15 Mention Density Gap Report — 2026 04 22
  Scan date: 2026 04 22 Method: grep across all wiki/ files (excluding scripts/), cross referenced against existing page slugs.
• Semantic Integrity Pass Log — 2026 04 18
  Scanned: ~409 pages (entities, concepts, analyses) Violations detected: 43 across 18 pages Fixed: 9 violations across 8 pages (mechanical rewrites to factual...
• Semantic Pass Resume — 2026 04 18
  | Audit | Detected | Fixed | Deferred | | | | | | | 1. Cureva/WikiBiome Boundary | 43 violations | 9 rewrites | 0 (34 verified factual) | | 2. Missing Interv...
• Shared Pathobionts Across Disease Signatures
  An analysis of which microbial taxa appear across multiple disease signatures in this knowledge base, what metal dependencies they share, and what the taxono...
• Stub Demotions — 2026 04 19
  Per §2f and Operational Rule 7, pages below source density threshold must carry `stub: true` + `stub_reason`. This batch fixes pages that were below threshol...
• Supersession Compliance Audit — 2026 04 18
  Entity/concept pages scanned: ~389 (all with ≥2 sources) Paragraphs with contradiction language: 30 Genuine supersessions applied: 2 Biological complexity (n...
• Wiki Health Check — 2026 04 14
  Automated run. Scope: full wiki (1,515 sources + 273 content pages). This report covers what improved since the April 13 lint, what remains unresolved, and w...
• Wiki Lint Report — 2026 04 13
  Automated lint run. Full scan of all wiki pages for structural integrity, broken references, missing pages, and coverage gaps.
• WikiBiome / Cureva — Gaps & Improvement Report 2026 04 12
  Generated: 2026 04 12 (automated scheduled run) Scope: Full audit of wiki content, raw paper library, index accuracy, and roadmap alignment Related: See also...
• WikiBiome / Cureva — Gaps & Improvement Report 2026 04 13
  Generated: 2026 04 13 (automated scheduled run) Scope: Full audit of wiki content vs prior report; new content since 2026 04 12; structural and coverage gaps...
• WikiBiome / Cureva — Gaps & Improvement Report 2026 04 14
  Generated: 2026 04 14 (automated scheduled run) Scope: Full audit of wiki content vs prior report; structural integrity checks; new opportunities identified ...
• WikiBiome Lint Report — 2026 04 12
  Automated health check run: 2026 04 12 Wiki pages scanned: 1,684 total (1,426 sources + 258 content pages) Issues found: 6 critical, 8 high priority, 5 mediu...
• WikiBiome Lint Report — 2026 04 13
  Automated health check run: 2026 04 13 Wiki pages scanned: 1,773 total (1,515 sources + 258 content pages) Issues found: 4 critical, 5 high priority, 7 mediu...
• WikiBiome Lint Report — 2026 04 14
  Scope: Full health check of 1,773 files (1,515 sources + 258 content pages) Run type: Automated scheduled task
• WikiBiome Lint Report — 2026 04 19
  Scope: Full health check of the vault at `~/Documents/Raw`. Run type: Weekly automated scheduled task (Sunday lint). Prior run: lint report 2026 04 14 (not l...
• WikiBiome Lint Report — 2026 04 21
  Scope: Full health check of the vault at `~/Documents/Raw`. Run type: Weekly automated scheduled task (Tuesday — slot shifted from Sunday 04 19 cycle). Prior...
• WikiBiome Lint Report — 2026 04 26
  Scope: Full health check of the vault at `~/Documents/Raw`. Run type: Weekly automated scheduled task (Sunday). Prior run: lint report 2026 04 21 (Tuesday sl...
• WikiBiome Lint Report — 2026 05 03
  Scope: Full health check of the vault at `~/Documents/Raw`. Run type: Weekly automated scheduled task (Sunday). Prior run: lint report 2026 04 26. Action pol...
• Zero Reference Pages Audit — 2026 04 19
  Karen, 2026 04 19, pointing at https://www.wikibiome.com/article/acidic microenvironment: > Why do any files on our website contain zero references? These re...