Axiom

OMICS governs multi-omic intelligence. Every signature evidenced. Every variant classified. Every analysis ledgered.

Constraints

MUST:     Compose all three primitives (INTEL + CHAT + COIN)
MUST:     Evidence-back every omic finding (GOLD/SILVER/BRONZE)
MUST:     Classify variants per ACMG/AMP standards
MUST:     Version all bioinformatics pipelines
MUST:     Trace gene expression signatures to source datasets (GEO series ID)
MUST:     Distinguish research-use from clinical-grade results
MUST:     Gate clinical decision support behind credentialed practitioners
MUST:     Ledger every analysis event (dataset, method, result, timestamp)
MUST:     Cite source databases with accession numbers
MUST:     Support temporal reclassification (variant evidence evolves)
MUST NOT: Present omic findings without evidence tier classification
MUST NOT: Generate clinical protocols without credentialed reviewer gate
MUST NOT: Diagnose or prescribe (decision SUPPORT, not decision MAKING)
MUST NOT: Store patient-identifiable genomic data in SHOP projection

Capabilities

INTEL_COMPOSE, PIPELINE_VERSION, SIGNATURE_EVIDENCE, VARIANT_CLASSIFY

COVERAGE: 255/255

SPEC

Purpose

OMICS is the multi-omic intelligence service.

OMICS resurfaces StarGEO’s NIH BD2K-funded crowdsourced gene expression annotation methodology as a governed data pipeline, extends it across five omic layers (genomics, transcriptomics, proteomics, metabolomics, epigenomics), and delivers clinician-ready decision support through governed CHAT channels gated by board-level credentialing.

StarGEO (2015-2023) proved that crowd-curation of open GEO data under FAIR principles produces peer-reviewed disease signatures (Nature Scientific Data 2017, doi:10.1038/sdata.2017.125). OMICS generalizes this methodology from transcriptomics to pan-omics, from crowdsourcing to governed AI reasoning, and from research-only to clinical decision support.

Structure

Root OMICS domains (conceptual sub-scopes, realized as LEARNING/IDF patterns):

SIGNATURES/   — Gene expression signatures from meta-analysis (StarGEO heritage)
VARIANTS/     — Variant interpretation pipeline (ACMG/AMP classification)
PATHWAYS/     — Metabolic pathway analysis (multi-omic integration)
PROTOCOLS/    — Clinician-ready intervention protocols (credential-gated)

Required closure artifacts per scope: CANON.md, README.md, OMICS.md, VOCAB.md, ROADMAP.md, COVERAGE.md, LEARNING.md.

Learning lane per governed scope: LEARNING.md at the scope root is terminal and SHALL NOT nest further LEARNING/.

Routes

web_docs:    https://hadleylab.org/
web_surface: https://hadleylab.org/SERVICES/OMICS/
web_app:     https://hadleylab.org/TALKS/OMICSCHAT/
magic:       magic://hadleylab.org/SERVICES/OMICS/

Data Contract

1. Omic analysis results are VAULT-gated by default (PRIVATE, credential-restricted)
2. Every analysis event is ledgered (who, when, dataset, method, result)
3. Public data source references (GEO IDs, ClinVar IDs) surface through SHOP
4. Patient-specific interpretations NEVER surface through SHOP
5. Evidence tiers: GOLD (published meta-analysis), SILVER (single-study validated), BRONZE (computational prediction)
6. Variant classifications MUST include ACMG criteria codes
7. Gene expression signatures MUST cite GEO series IDs

Data Sources

Ecosystem Connectivity

1. Upstream: SERVICES governance contracts, GENOMICS + MEDICINE vertical constraints (canonic-canonic).
2. CLINICAL plane: patient biomarker data feeds omic analysis (VAULT-gated).
3. TALK plane: OMICSCHAT channel delivers decision support conversations.
4. LEARNING plane: discovered patterns (signatures, pathways, variant reclassifications) backpropagate.
5. LEDGER plane: every analysis event (dataset + method + result) ledgered immutably.
6. COIN plane: per-analysis COIN events (work measured and minted).
7. AUTH plane: board-level certification required for clinical protocol generation.
8. KYC plane: clinician credential verification (board certification + state licensing).
9. External: GEO, ClinVar, PharmGKB, COSMIC, GTEx, TCGA, PubMed public APIs.

Pages

Default: Overview.

INTEL

Proxy Architecture

Proxy Routes

LEDGER Integration

Every proxy query MUST:

1. Append to ledger:OMICS:{source} via appendToLedger()
2. Include upstream source, query parameters, response status
3. Backpropagate to LEARNING.md as pattern row

Signal mapping:

NCBI query     → OMICS_QUERY (source: ncbi, dataset: geo|clinvar|pubmed)
PharmGKB query → OMICS_QUERY (source: pharmgkb)
Analysis event → OMICS_ANALYSIS (method, dataset, result_hash)

Evidence Tier Classification

Data Source Intelligence

Test

LEARNING

Ledger

Meta-Patterns

Constraints

1. MUST log every methodology discovery to this ledger
2. MUST cite source of learning
3. MUST NOT overwrite — append only
4. SHOULD propagate shared patterns to MEDCHAT, MAMMOCHAT, ONCOCHAT

ROADMAP

VOCAB

INHERITANCE CHAIN

SERVICES

SERVICES compose primitives — INTEL + CHAT + COIN. Every service governed. Every scope discovered.

MUST:     Maintain TRIAD integrity (CANON.md + VOCAB.md + README.md)
MUST:     Treat SPEC as scope identity (`{SCOPE}` directory), not as a file
MUST:     Every SERVICE scope include ROADMAP.md, COVERAGE.md, LEARNING.md, and `{SCOPE}.md` as governed content surfaces
MUST:     Discover SERVICE scopes from filesystem only (no manual catalog)
MUST:     Keep http:// and magic:// on the same namespace (transport differs, scope path matches)
MUST:     CANON.md = axiom + universal constraints (no service names, no paths, no implementation)
MUST:     README.md = how to run the CANON (nothing else)
MUST:     {SCOPE}.md = SPEC — the interface (purpose, routes, projections, ecosystem)
MUST:     SHOP.md = public projection file (per scope, filesystem-discoverable)
MUST:     VAULT.md = private projection file (per scope, filesystem-discoverable)
MUST:     Runtime implementation remains under ~/.canonic; this workspace is governance-first
MUST NOT: Hardcode service names in CANON constraints (law speaks universals)
MUST NOT: Define ungoverned terms outside VOCAB.md
MUST NOT: Treat `{SCOPE}.md` as SPEC identity
MUST NOT: Move architecture/lifecycle into README
MUST NOT: Leak private projections to public surfaces
MUST NOT: Maintain duplicate mapping tables outside generated manifest outputs
MUST NOT: Add runtime jargon to governance contracts
MUST:     Ledger-consuming services declare source ledgers, scope filters, and closure gates
MUST:     Learning governance remains live — closure claims require fresh DISCOVER → GENERATE → RELINK evidence

hadleylab-canonic

HADLEYLAB ships software. Every app, book, paper, deal, and patent is PROOF that MAGIC works. COIN = WORK. LEARNING = COMPUTE.

MUST:     Every app, book, paper, deal, or patent is evidence of MAGIC
MUST:     All scopes inherit canonic-canonic/CANONIC.md governance
MUST:     All users governed under USERS/ via SERVICES/USER
MUST:     Cross-index INTEL across users (INTEL.md)
MUST:     Shared events propagate to ALL affected user dashboards
MUST:     Maintain governance workspace purity (.md files only)
MUST:     Ledger all COIN (validated work) through MAGIC 255
MUST:     Compile all INTEL from governed sources
MUST:     Keep frontend/runtime implementation under ~/.canonic (hidden runtime)
MUST:     Surface governed TALK, Library, and SERVICES scopes (no orphan content)
MUST:     Derive nav labels from governed scope names (no hardcoded strings)
MUST NOT: Publish without governance (CANON.md required)
MUST NOT: Duplicate primitives — compose from INTEL, CHAT, COIN
MUST NOT: Silo intelligence inside a single user when multiple are affected
MUST NOT: Expose VAULT contents outside NDA scope
MUST NOT: Store runtime artifacts in governance workspace

canonic-canonic

SPEC is governance. `canonic-canonic/` is the spec root.

MUST:     Keep this repo governance-only (.md/.pdf)
MUST:     Publish workspace mapping in CANONIC.git (no hardcoded repo lists)
MUST:     Preserve three primary lanes: FOUNDATION, INDUSTRIES, MAGIC
MUST NOT: Commit runtime artifacts here (runtime belongs in ~/.canonic/)
MUST:     Sell MAGIC tiers — the product, not the proof (proof is hadleylab-canonic)
MUST NOT: Embed beta-test app URLs in platform page content