MethylAsk

A web tool that reads a person's methylation/epigenomic file, matches the markers against public scientific databases, and produces a readable report of what is known about them — clinical relevance and popular-interest findings side by side, each tagged with an evidence tier.

Runs on a local server or private cloud so personal data stays under the operator's control.

Status

Prototype scaffold. See docs/DESIGN.md for the full architecture and docs/VALIDATION.md for live data-source validation results.

Built on bio-core

MethylAsk depends on bio-core for all organism-agnostic mechanism — the provider interface and registry, evidence tiering, the HTML/PDF report renderer, and the resumable fetch helper. MethylAsk itself holds only the human-methylation knowledge: the methylation databases it queries, the epigenetic clocks, and the Illumina-array normalization.

methylask/
  providers/    methylation-specific providers (EWAS Catalog, ClinVar, GDC)
                — each imports the shared Provider/Finding/Tier from biocore
  ingest/       file-format parsers (CSV/GEO, IDAT, bedMethyl, ...)
  normalize.py  probe/rsID → canonical genome coordinate (bundled manifests)
  clocks.py     epigenetic-clock engine (Horvath, Hannum, PhenoAge, ...)
  cli.py        `methylask status|refresh|report`
data/reference/ small static reference files committed to the repo (<100 MB)
scripts/        refresh + build CLIs
docs/           design, validation, disclaimer

The provider registry, evidence tiering, and report renderer live in bio-core (biocore.providers, biocore.report) and are imported, not duplicated.

Install

MethylAsk depends on the private GoodAncestor/bio-core repo, declared as a git-source dependency in pyproject.toml. A plain pip install . resolves it from GitHub, so the machine needs git access to the private repo (an SSH key or a token in the git credential helper). Two ways:

# A) let pip pull bio-core from GitHub (needs private-repo git access)
pip install .

# B) develop against a local bio-core checkout instead
git clone https://github.com/GoodAncestor/bio-core.git ../bio-core
pip install -e ../bio-core
pip install -e . --no-deps        # bio-core already satisfied locally

Quick start

methylask status                     # provider health + cache ages
methylask refresh --provider all     # build/refresh local caches
methylask report sample.csv --pdf    # produce a report from a sample

Data

Small static reference files (array manifests, clock coefficients) live in this repo. Large corpora (GDC/TCGA methylation, ClinVar, EWAS Catalog dump) are mirrored to local server disk by methylask refresh — see docs/DESIGN.md §3.4.

Disclaimer

MethylAsk reports research associations, not medical diagnoses. See docs/DISCLAIMER.md — the single source of truth for all disclaimer language.