OMICS

OMICS

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

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-canonic.github.io/
web_surface: https://hadleylab-canonic.github.io/SERVICES/OMICS/
web_app:     https://hadleylab-canonic.github.io/CHAT/OMICSCHAT/
magic:       magic://hadleylab-canonic.github.io/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

Source Type Endpoint Proxy Format
NCBI GEO Gene expression data (2M+ samples) eutils.ncbi.nlm.nih.gov/entrez/eutils/ api.canonic.org/omics/ncbi/ REST/JSON
ClinVar Variant classifications eutils.ncbi.nlm.nih.gov/entrez/eutils/ api.canonic.org/omics/ncbi/ REST/JSON
PharmGKB Pharmacogenomics (drug-gene) api.pharmgkb.org/v1/data/ api.canonic.org/omics/pharmgkb/ REST/JSON
COSMIC Somatic mutations (cancer) cancer.sanger.ac.uk/cosmic/api/ — REST/JSON
GTEx Tissue-specific expression gtexportal.org/api/v2/ — REST/JSON
TCGA Cancer genomics api.gdc.cancer.gov/ — REST/JSON
PubMed/PMC Research corpus eutils.ncbi.nlm.nih.gov/entrez/eutils/ api.canonic.org/omics/ncbi/ REST/JSON
ClinicalTrials.gov Active trials clinicaltrials.gov/api/v2/studies — REST/JSON
Disease Ontology (DOID) Disease taxonomy disease-ontology.org — OBO/JSON

Ecosystem Connectivity

  1. Upstream: SERVICES governance contracts, GENOMICS + MEDICINE vertical constraints (canonic-canonic).
  2. HEALTH 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

Page Sections
Overview Purpose, Structure
Data Routes, Data Contract, Data Sources
Ecosystem Ecosystem Connectivity

Default: Overview.

*OMICS SPEC SERVICES*
TALK AUTO