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 what is newly flagged today.

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Summary Table

CategoryIndex ClaimsActualStatus
Sources1,5151,515✅ Accurate
Entities130135🔴 Stale (+5)
— Metals/Metalloids1717✅
— Microbes8082🟡 Stale (+2)
— Fungi46🔴 Stale (+2)
— Archaea11✅
— Diseases2829🟡 Stale (+1)
Concepts8890🟡 Stale (+2)
Disease Signatures1515✅ Accurate
Interventions1313✅ Accurate
STOPs1114🔴 Stale (+3)
Analyses1010✅ Accurate

Index must be updated: Entities (+5), Concepts (+2), STOPs (+3).

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🔴 Critical Issues

1. All 1,515 Source Pages Missing v2 Frontmatter Fields

Every source page in the vault is missing the following v2-required fields:

  • `evidence_level` — 0/1,515 populated
  • `karen_brain_primitives` — 0/1,515 populated
  • `key_findings` — 0/1,515 populated
  • `metals_discussed` — 0/1,515 populated
  • `taxa_discussed` — 0/1,515 populated

Impact: Cureva's pipeline cannot filter sources by evidence level or reasoning primitive. Cross-condition pattern detection cannot run. This is the known Priority 5 migration backlog.

Action: Batch inference run needed. These fields can be inferred programmatically from existing page content (evidence level from study design language, primitives from metals/taxa mentioned). See CLAUDE.md §11 Migration Plan.

Grep command used: `grep -rl "^evidence_level:" wiki/sources/ | wc -l` → 0

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2. Akkermansia Misspelling in Parkinson's Signature — Still Unresolved

`parkinsons-disease.md` references `akkermansia mucinicola` — this entity does not exist. The correct name is `akkermansia muciniphila`.

Occurrences: 2 uses in `parkinsons-disease.md` (taxonomic signature section and virulence table).

Fix: Find/replace `akkermansia-mucinicola` → `akkermansia-muciniphila` in `wiki/signatures/parkinsons-disease.md`.

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3. DOI Quality Issues in Source Pages

IssueCount
`doi: ""` (empty)28
`doi: "various"`24
`doi: "N/A"`2
Total problematic54

Sources with `doi: "various"` are typically batch-summary pages created before individual paper ingestion. Sources with empty DOIs need manual lookup or should be flagged as `doi: "not yet verified"` per v2 spec.

Notable examples: `metabolic-pathways-2023-2025-gut-microbiome-t1d.md`, `fmt-2025-promising-treatment-t2d-insulin-resistance.md`, `high-fiber-diet-2025-gut-microbiome-diabetes-interventions.md`

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🟡 Significant Gaps

4. Index Stale — 5 Entity + 2 Concept + 3 STOP Pages Not Listed

Missing from index entity listings:

  • Entities: 5 new pages created since last index update (actual 135 vs claimed 130). The new fungi/archaea entities (candida-albicans, candida-auris, candida-tropicalis, debaryomyces, methanobrevibacter-smithii, saccharomyces-cerevisiae, torulaspora) account for the discrepancy.
  • Concepts: 2 new concept pages not in index (actual 90 vs claimed 88).

Missing from index STOP listings (3 STOPs not included):

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5. Seven Entity Pages Missing Core v2 Fields

The following entity pages (all fungi/archaea added recently) are missing `seo_target`, `wikipedia_differentiation`, and `last_substantive_update`:

  • `candida-albicans.md`
  • `candida-auris.md`
  • `candida-tropicalis.md`
  • `debaryomyces.md`
  • `methanobrevibacter-smithii.md`
  • `saccharomyces-cerevisiae.md`
  • `torulaspora.md`

These are high-value pages (Candida species appear in multiple signatures). Each needs an `seo_target` query and a one-line `wikipedia_differentiation` statement before WikiBiome deployment.

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6. Six Intervention Pages Missing `karen_brain_primitives` and `last_substantive_update`

The following intervention pages were created without full v2 frontmatter:

  • `mediterranean-diet.md`
  • `probiotics-asd-dysbiosis.md`
  • `probiotics-general.md`
  • `selenium-supplementation.md`
  • `vitamin-d-supplementation.md`
  • `zinc-supplementation.md`

These are all clinically important pages. Missing `karen_brain_primitives` means Cureva cannot retrieve them by pipeline step.

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7. Seven Signature Pages With No Linked Interventions

The following signature pages have `validated_interventions: []`:

  • `alzheimers-disease.md`
  • `autism-spectrum-disorder-microbiome-signature.md`
  • `cardiovascular-disease.md`
  • `colorectal-cancer.md`
  • `obesity.md`
  • `parkinsons-disease.md`
  • `type-2-diabetes.md`

Impact: Cureva cannot surface intervention recommendations for these conditions. These represent 7 of the 15 signatures — nearly half the platform's clinical value is blocked.

Priority order by source library size: Type-2 Diabetes (30 sources), Parkinson's (118 sources in vault), Alzheimer's (large library), CRC, CVD, Obesity, ASD (173 sources — largest single condition library).

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8. Eight Signature Pages With No Linked STOPs

Signatures with `stops: []` or missing stops field:

  • `alzheimers-disease.md`
  • `autism-spectrum-disorder-microbiome-signature.md`
  • `cardiovascular-disease.md`
  • `colorectal-cancer.md`
  • `depression.md` (field absent from frontmatter)
  • `obesity.md`
  • `parkinsons-disease.md`
  • `type-2-diabetes.md`

Note on `depression.md`: The `validated_interventions` and `stops` fields are absent from the frontmatter entirely (not just empty arrays). This needs to be added.

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9. All 29 Disease Entities Missing `signature_page` Frontmatter Field

Every disease entity page is missing the `signature_page:` field in frontmatter. This field enables platform routing (WikiBiome → Cureva cross-link). Even for diseases without a signature yet, the field should be present as blank or pointing to a planned page.

Disease entities that DO have a companion signature: alzheimers, autism-spectrum-disorder, cardiovascular-disease, colorectal-cancer, crohns-disease, depression, endometriosis, graves-disease, hashimotos-thyroiditis, multiple-sclerosis, obesity, pancreatic-cancer, parkinsons-disease, pcos, type-2-diabetes (15 total).

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10. All 90 Concept Pages Missing v2 Fields

The entire concept library (90 pages) is missing:

  • `karen_brain_primitives` — 0/90
  • `seo_target` — 0/90
  • `last_substantive_update` — 0/90

This is a known Priority 6 migration item. Concepts without `karen_brain_primitives` cannot be retrieved by Cureva's pipeline step.

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11. 118/135 Entity Pages Missing `source_count` Field

Only 17 entity pages have a `source_count` field. The remaining 118 need this added. Some that do have it show mismatches (e.g., `aluminum.md` declares `source_count: 14` but has an inline sources list in different format — needs verification).

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🟢 Lower Priority Observations

12. High-Priority Diseases Lacking Signature Pages

The following diseases have large source libraries but no companion signature page. These represent significant untapped Cureva value:

DiseaseSources Referencing It
Type 1 Diabetes~99
Chronic Kidney Disease~97
Postpartum Depression~40+ condition-matched
Schizophrenia~66
Ovarian Cancer~75
Hypertension~48
GERD~41
Breast Cancer~17
Ulcerative Colitis~12
Rheumatoid Arthritis~12
IBS~8
Celiac Disease~3

Recommendation: Prioritize Type 1 Diabetes, CKD, and Postpartum Depression signatures next — each has 40+ sources and a complete entity page already in place.

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13. Missing Concept and Entity Pages Referenced by Wikilinks

The following pages are linked from signatures/entities but do not exist:

Concepts/entities that need pages:

Several of these are referenced in signature `validated_interventions` lists but have no intervention page — meaning the signature links are broken.

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14. Near-Orphan Entity: `lachnospira.md`

`lachnospira.md` has only 1 inbound link. `lachnospiraceae.md` is the more commonly referenced entity. This may be a duplicate or a page that needs promotion into more signature pages.

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✅ Issues Resolved Since April 13

  • Backslash-broken wikilinks in `dietary-metal-microbiome-interactions.md` — ✅ Fixed
  • Metal entity pages missing `subtype:` field — ✅ All metal/metalloid entities now have subtype
  • Missing entity stubs (bacteroides-thetaiotaomicron, candida-auris, candida-tropicalis, aeromonas) — ✅ Stub pages now exist (though lacking full v2 fields)
  • Index source count — ✅ 1,515 accurate
  • All 15 signature pages have full v2 confidence blocks — ✅ Confirmed
  • All 14 STOP pages have complete frontmatter — ✅ Confirmed
  • New ASD-related stops added (stop-iron-supplementation-asd) — ✅ Confirmed

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Action Priority Queue

Immediate (before next content session):

  1. Fix `akkermansia-mucinicola` → `akkermansia-muciniphila` in `parkinsons-disease.md` (2 occurrences)
  2. Update index: add 5 entities, 2 concepts, 3 STOPs to listings; update counts table
  3. Add `validated_interventions` and `stops` fields to `depression.md` frontmatter

High priority (next 1–2 sessions):

  1. Add `karen_brain_primitives` and `last_substantive_update` to 6 intervention pages
  2. Add `seo_target`, `wikipedia_differentiation`, `last_substantive_update` to 7 fungi/archaea entity pages
  3. Create intervention pages for conditions listed in signatures but lacking pages (lactoferrin-supplementation, hbot, faecalibacterium-restoration, berberine-methimazole, high-fiber-prebiotics)
  4. Add `signature_page:` field to all 29 disease entity frontmatters

Medium priority (migration batch work):

  1. Add `signature_page` links for the 15 diseases with existing signatures
  2. Begin source page v2 migration: batch-infer `evidence_level`, `karen_brain_primitives`, `metals_discussed` for highest-traffic condition source libraries (start with Parkinson's 118, ASD 173, T2D 30)
  3. Add `source_count` field to 118 entity pages missing it

Longer term:

  1. Build signature pages for T1D, CKD, Postpartum Depression, Schizophrenia (high source support)
  2. Add `karen_brain_primitives` and `seo_target` to all 90 concept pages
  3. Resolve 54 source pages with problematic DOIs (empty, "various", "N/A")

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Automated health check — 2026-04-14. Grep commands used are noted inline. No content was modified during this run.

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