# OpenEndo

> Open data hub for endometriosis research — clinical trials, papers, funding & policy, refreshed weekly from ClinicalTrials.gov and PubMed. Open source, MIT, built for patients, researchers and policymakers.
>
> **Deployment note:** the public UI (openendo.org) is a Lovable app — repo files are NOT served there. All links below are raw.githubusercontent URLs (the only working public paths for repo content).

RAW = https://raw.githubusercontent.com/wckdboy/openendo/main

## Agents: start here
- [CHECKPOINT.md](https://raw.githubusercontent.com/wckdboy/openendo/main/CHECKPOINT.md): living task board — current focus, horizon tasks, blockers, change log (READ FIRST)
- [AGENTS.md](https://raw.githubusercontent.com/wckdboy/openendo/main/AGENTS.md): repo rules for agents

## Live product (openendo.org — Lovable app in wckdboy/openendo-www)
The public UI is NOT served from this repo. GitHub Pages CNAME-redirects; `docs/*.html` paths on openendo.org 404.
- Home: https://openendo.org/
- Dashboard: https://openendo.org/dashboard
- Research explainer (fetches `what-we-know.html` live): https://openendo.org/research
- Access finder (fetches `access.json` live): https://openendo.org/access
- Knowledge (fetches `docs/knowledge/index.md` + listed pages live; bundled fallback): https://openendo.org/knowledge
- Danish locale: https://openendo.org/da and the `/da/...` twins of the routes above

## Legacy static HTML (NOT the product UI — kept as source / unique pages)
- [**What we know / what we don't — research explainer (visual)**](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/what-we-know.html): **LIVE CONTRACT** — `/research` fetches this file. Do not delete. Fonts: `docs/assets/fonts/`. PDF: `docs/what-we-know.pdf`
- [One-pager for decision-makers (DA)](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/one-pager-dk.html): unique advocacy page; no Lovable route yet — keep
- [One-pager for decision-makers (EN)](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/one-pager-en.html): unique; keep
- [How to support](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/support.html): seven ways to contribute; no `/support` route — keep
- [AI & compute agenda](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/ai-agenda.html): unique; keep
- [Style guide](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/styleguide.html): visual brand (companion: BRAND.md); keep
- [Knowledge hub (human, legacy HTML)](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/wiki.html): catalog of `docs/knowledge/*.md`. Live `/knowledge` fetches the markdown (not this file) with a bundled fallback
- [Dashboard (legacy HTML)](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/index.html): superseded by `/` + `/dashboard`; kept as CSS/nav/brand host for the leftovers

## Machine-readable data (JSON)
- [Data layer contract](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/README.md): file → content → source → cadence → owner (agents: read before editing datasets)
- [Identifier rules](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/IDENTIFIERS.md): read before touching any dataset — NCT/PMID/CHEMBL/UniProt kept verbatim, never invented
- [Recruiting trials worldwide](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/trials_global_recruiting.json) — generated weekly
- [All registered trials in Denmark](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/trials_denmark.json)
- [New/updated trials, last 7 days](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/trials_recent.json)
- [New papers, last 7 days](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/pubmed_recent.json)
- [Papers per month, 6 months](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/pubmed_monthly.json)
- [Drug-target landscape (58 targets, ChEMBL-verified)](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/targets.json)
- [Repurposing candidates — 9 M3 shortlisted pairs with validation status](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/repurposing_candidates.json) (top-tier / watchlist / validated-axis / wrong-direction; ranked shortlist + verdicts: [m3-validation.md](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/evidence/m3-validation.md))
- [Funding opportunities with deadlines](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/funding.json)
- [Access finder — country/postcode → meds, centres, help](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/access.json) — DK full, GB/US/DE orgs (schema openendo-access-v1)
- [Editorial content (EN/DA)](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/content.json)
- [Generation metadata](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/meta.json)
- [RO-Crate manifest (FAIR packaging of all datasets)](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/data/ro-crate-metadata.jsonld)

## Knowledge base
> Knowledge pages are raw markdown — **live contract** for openendo.org/knowledge (index.md + listed pages; bundled fallback). Human hub leftover: wiki.html. SCHEMA first.
- [SCHEMA](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/SCHEMA.md): conventions for creating/editing knowledge pages (agents must read)
- [Entities — ryeqo](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/entities/ryeqo.md): relugolix combo, EU-approved, generelt tilskud in DK
- [Entities — yselty](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/entities/yselty.md): linzagolix, EU-approved Dec 2024, no general reimbursement for endometriosis in DK (verified 2026-09-02)
- [Entities — hmi-115](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/entities/hmi-115.md): first non-hormonal therapy in Phase 3
- [Entities — my-endo-trial](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/entities/my-endo-trial.md): NCT06211231 — digital mindfulness/acceptance self-management, recruiting in Denmark
- [Entities — sirolimus](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/entities/sirolimus.md): mTOR inhibitor, M3 repurposing rank 1 — mTOR/ovarian-senescence evidence; GEO reanalysis confirms FKBP4 2.2x down in lesions; no registered endo trial
- [Concepts — gnrh-antagonists](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/concepts/gnrh-antagonists.md): the class behind Ryeqo/Yselty
- [Concepts — saliva-diagnostics](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/concepts/saliva-diagnostics.md): non-invasive testing vs diagnostic delay
- [Concepts — ferroptosis](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/concepts/ferroptosis.md): iron-dependent cell death — SEMA3C paper, GPX4/SLC7A11 targets, sulfasalazine convergence
- [Concepts — computational-drug-repurposing](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/concepts/computational-drug-repurposing.md): simvastatin/primaquine POC + M3 ChEMBL screen (9 pairs)
- [Concepts — mrgprx2-pain](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/concepts/mrgprx2-pain.md): mast-cell MRGPRX2/histamine/TRPV1 pain axis — cetrorelix hit is target-validating; GEO reanalysis confirms mast-cell markers 11-15x enriched in lesions
- [Concepts — diversity-gap](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/concepts/diversity-gap.md): under-representation of racial/ethnic minorities in endo research + trials; access bias, not biology (5 PMIDs, 2017-2025)
- [Concepts — danish-registries](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/concepts/danish-registries.md): DNPR/Rx/MBR/psychiatric registers; CPR-linkage; diagnostic delay, obstetric outcomes, mental health burden; registry analytics entry point (7 PMIDs, 2017-2026)
- [Comparisons — ryeqo vs yselty](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/knowledge/comparisons/ryeqo-vs-yselty.md)

## Research (Percival's workstream, merged)
- [M1 fold-input pack](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/structures/fold_input/README.md): 35 novel drug targets, AlphaFold-ready
- [M1 AlphaFold run decision memo](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/structures/fold_input/af2-decision.md): corrected 2026-09-03 coverage audit — 34/35 in AFDB + GPX4 experimental → 0 to fold, $0
- [Virtual testing pipeline](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual-testing.md): structure/docking/MD validation ladder + infra + phases
- [Phase 0 audit — structure & expression coverage](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase0.md): AFDB coverage (corrected 2026-09-03: 34/35 + GPX4 in PDB — see af2-decision.md), PDB structures for all M3 targets, HPA, ChEMBL (+ [machine data](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase0.json))
- [Phase 0.5 — lesion expression reanalysis (GEO)](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase0.5.md): COMPLETE 2026-09-03 — GSE282532 (endometrioma bulk): FKBP4 2.2x down, mast-cell markers 11–15x up, SLC7A11 2x down; GSE247695 (scRNA) + GSE263897 (GeoMx spatial, [`gse263897_targets.json`](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/gse263897_targets.json)): mast-cell enrichment is endometrioma-specific, absent in superficial peritoneal lesions; FKBP4 stroma-down/epithelium-up replicated
- [Phase 1.0 — docking (Vina)](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase1/phase1.md): DONE 2026-09-04 ($0) — sulfasalazine→xCT −8.52 (binds; WATCHLIST selectivity issue unchanged), rapamycin→FKBP52/FKBP4 −6.38 vs FKBP12 −7.06 (FKBP4 engages sirolimus ~as well as FKBP12); native-redock calibrations; cetrorelix→MRGPRX2 deferred to Phase 2 (tool boundary, documented). Machine data: [`docking_results.json`](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase1/docking_results.json) · [`admet_profile.json`](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase1/admet_profile.json) (9 M3 candidates) · [`poses/`](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase1/poses/) (top poses, MD-ready)
- [Phase 2 — OpenMM run package](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase2/phase2-plan.md): READY 2026-09-12, **not started** (no trajectories; human GPU budget still open). Recommended first job P2-A: 100 ns FKBP12 crystal-RAP control + 100 ns FKBP52 Vina pose. Machine data: [`phase2-plan.json`](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase2/phase2-plan.json) · assembled inputs under [`phase2/inputs/`](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/virtual/phase2/inputs/)
- [M2 living evidence — digest](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/evidence/digest-2026-09-11.md): weekly evidence synthesis (PubMed E-utilities; prior: 09-04)
- [M2 evidence weekly data](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/evidence/weekly/2026-09-11.json): machine-readable evidence snapshot
- [M3 repurposing screen digest](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/evidence/digest-2026-09-02.md): 9 drug-repurposing candidates (M3 validation: m3-validation.md)
- [T7 lab software modernization track](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/lab-software-modernization.md): Danish lab software roadmap
- [Integration contract — RO-Crate](https://raw.githubusercontent.com/wckdboy/openendo/main/docs/research/tools-and-integration.md): how the hub plugs into ELN/LIMS/repositories

## Contributing
- [CONTRIBUTING](https://raw.githubusercontent.com/wckdboy/openendo/main/CONTRIBUTING.md): PR checklist, quality bar, review workflow
- [BRAND](https://raw.githubusercontent.com/wckdboy/openendo/main/BRAND.md): machine-readable brand spec for agents
- [LICENSE](https://raw.githubusercontent.com/wckdboy/openendo/main/LICENSE): MIT — the data is a public good