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Permea Core OSS Operating System PR Summary

1. PR Purpose

This branch adds the first Permea Core OSS operating system: a public documentation layer for open scientific governance, contributor workflow, claim hygiene, dataset/release safety, paper alignment, derivative project governance, and citation/versioning/archive practice.

The branch is documentation-only. It does not add scientific results, model outputs, datasets, wet-lab evidence, or public preprint readiness claims.

2. What This Branch Adds

This branch adds:

  • root OSS community files
  • scientific governance policies
  • paper and release alignment policies
  • contributor, authorship, dry-lab, and wet-lab collaboration policies
  • community, maintainer, reviewer, and reviewer credit policies
  • derivative project governance
  • citation, versioning, archive/deprecation, and attribution policies
  • a README index for the operating docs

3. File Groups Added

Root files:

  • CONTRIBUTING.md
  • CODE_OF_CONDUCT.md
  • SECURITY.md
  • SUPPORT.md
  • CITATION.cff

Planning and map:

  • docs/OSS_OPERATING_DOCS_MAP.md

Scientific governance:

  • docs/scientific-governance/CLAIM_REGISTRY.md
  • docs/scientific-governance/DATASET_POLICY.md
  • docs/scientific-governance/PUBLIC_SAFE_ARTIFACT_POLICY.md
  • docs/scientific-governance/REPRODUCIBILITY_GUIDE.md

Paper and release:

  • docs/paper-alignment/PAPER_ALIGNMENT_POLICY.md
  • docs/release/RELEASE_REVIEW_PROCESS.md
  • docs/release/PUBLIC_RELEASE_CHECKLIST.md
  • docs/release/RELEASE_OWNERSHIP_MATRIX.md
  • docs/release/VERSIONING_POLICY.md
  • docs/release/ARCHIVE_AND_DEPRECATION_POLICY.md
  • docs/release/ATTRIBUTION_POLICY.md

Contributor and collaboration:

  • docs/contributors/CONTRIBUTOR_LEVELS.md
  • docs/contributors/AUTHORSHIP_POLICY.md
  • docs/contributors/DRY_LAB_CONTRIBUTION_POLICY.md
  • docs/contributors/WET_LAB_COLLABORATION_POLICY.md

Community governance:

  • docs/community/COMMUNITY_GOVERNANCE.md
  • docs/community/MAINTAINER_GUIDE.md
  • docs/community/REVIEWER_WORKFLOW.md
  • docs/community/REVIEWER_CREDIT_POLICY.md

Derivative projects:

  • docs/derivatives/DERIVATIVE_PROJECT_POLICY.md
  • docs/derivatives/PROJECT_REGISTRY.md
  • docs/derivatives/DERIVATIVE_REVIEW_CHECKLIST.md

4. What This Branch Does Not Claim

This branch does not claim:

  • completed wet-lab validation
  • clinical efficacy
  • therapeutic efficacy
  • universal delivery prediction
  • production-grade drug delivery platform status
  • AlphaFold-level performance, adoption, or standardization
  • dataset redistribution permission
  • public preprint readiness
  • legal conclusions about licensing, IP, employment, trademark, university policy, or authorship disputes

"AlphaFold for Delivery" may be used only as ambition or positioning, not as a maturity claim.

5. Review Checklist

  • README index links resolve.
  • Added docs are documentation-only.
  • No data, model, result, figure, or benchmark artifacts are added.
  • No secrets, credentials, private records, or restricted artifacts are exposed.
  • Policy docs use consistent role and release terminology.
  • Deferred items are visible rather than silently resolved.

6. Claim Hygiene Checklist

  • Claims remain scoped to governance and operating infrastructure.
  • Benchmark claims remain scoped to dataset, split, metric, model, artifact, and evidence level.
  • No wet-lab validation is claimed unless documented.
  • No clinical efficacy is claimed.
  • No universal delivery prediction is claimed.
  • No AlphaFold-level maturity, adoption, or standardization is claimed.
  • Permea-aligned does not mean Permea-validated.

7. Dataset / Public-Safe Artifact Checklist

  • Dataset redistribution permission is not claimed.
  • Row-level datasets remain blocked unless explicit permission and review are documented.
  • Row-level labels, features, predictions, rankings, split manifests, group assignments, leakage tables, and raw upstream mirrors remain held unless release-safe.
  • Aggregate artifacts are still subject to claim-boundary review.
  • Dataset/source/license uncertainty routes to Hold or manual review.

8. Contributor / Community Checklist

  • GitHub contribution does not automatically grant authorship.
  • Attribution does not equal authorship.
  • Attribution does not equal endorsement.
  • Reviewer input does not equal peer review or external validation.
  • Wet-lab collaboration interest does not equal wet-lab validation.
  • Maintainer, reviewer, release approver, and founder/manual approver roles are separated.

9. Release-Readiness Checklist

  • Release gates are documented.
  • Release ownership matrix is present.
  • Public release no-go conditions are explicit.
  • Versioning, archive, correction, withdrawal, and deprecation states are documented.
  • Citation guidance avoids invented DOI/archive metadata.
  • Public release requires recorded approval where applicable.

10. Known Deferred Items

  • exact maintainer/release approver roster
  • formal legal/licensing workflow
  • formal trademark/branding process
  • derivative project templates
  • Zenodo/DOI/archive setup
  • final citation metadata
  • project-specific maintainer assignments

11. Recommended Reviewer Focus

Reviewers should focus on:

  • whether the policy set is internally consistent
  • whether README links and docs paths are correct
  • whether claim boundaries are conservative enough
  • whether dataset/public-safe artifact restrictions are explicit enough
  • whether maintainer/reviewer/release roles are practical
  • whether deferred legal, branding, citation, and roster items are clearly marked

12. Merge Readiness Note

This branch is suitable for review as a documentation-only OSS operating foundation package if the README index and policy links are correct.

Merge should not be treated as public scientific validation, dataset release approval, wet-lab validation, clinical readiness, public preprint readiness, or endorsement of derivative projects.