QTLos DomainOS

Status: Scaffold (routing wired, skills pending)
Engine: hordago-qtlos
Domain: Molecular QTL mapping (eQTL, caQTL, mQTL, haQTL, allelic imbalance)

Molecular-QTL DomainOS: eQTL / caQTL / mQTL / haQTL mapping and allelic-imbalance analysis. Routing is wired with status=scaffold; requests degrade to the pubmed + chembl + open-targets MCP fallback until skills land.

Field	Value
Product	QTLos
Engine id	hordago-qtlos
Intent key	qtlos
Repository	Hordago-Labs/hordago-qtlos
Plugin	hordago-qtlos
Maturity (registry)	Scaffold (routing wired, skills pending)

Overview

Molecular-QTL DomainOS: eQTL / caQTL / mQTL / haQTL mapping and allelic-imbalance analysis. Routing is wired with status=scaffold; requests degrade to the pubmed + chembl + open-targets MCP fallback until skills land.

Scientific approach

QTLos structures every run as 5 phases. Gates marked HITL require an explicit human-in-the-loop approval before the run advances.

#	Phase	Gate	HITL
1	Molecular Phenotyping	Quantify molecular phenotype (expr/chrom).	No
2	Genotype Harmonization	Harmonize genotypes and covariates.	No
3	QTL Mapping	Map cis/trans QTLs.	No
4	Allelic Imbalance	Test allelic imbalance.	No
5	Colocalization	Colocalize with GWAS loci.	Yes

Capabilities & evidence objects

Domain tools / skills

• eqtl-mapping
• caqtl-mapping
• allelic-imbalance
• colocalization

Evidence objects

Object	Role	Consumer
result.json	planned	co-writer

Canonical artifacts (5-artifact contract)

Planned

The 5-artifact contract below is the target shape. Canonical-artifact emission is tracked as inherited debt (Wave 3C) and is not yet guaranteed.

Artifact	Description
result.json	Structured primary result payload for the domain run.
report.md	Human-readable narrative summary of the analysis.
provenance.json	Tool versions, reference data, and algorithm lineage for reproducibility.
gate_status.json	Per-phase gate pass/fail decisions.
session_summary.json	Session metadata for replay and audit.

Standalone quickstart

Zero platform dependency

This quickstart runs the DomainOS standalone. The Hordago platform is not required; platform composition is opt-in (see Composition below).

1. Install the standalone hordago-qtlos plugin (Hordago-Labs/hordago-qtlos) -- no Hordago platform required.
2. Invoke the domain skill with a QTLos intent (see the intent keywords below).
3. Review the emitted artifacts under the run's output directory.

Intent keywords (route to this engine):

qtlos qtl.?os\b hordago-qtlos qtl validation caqtl eqtl mqtl haqtl allelic imbalance analyze.+qtl data

Worked example

cis-eQTL mapping with GWAS colocalization (planned surface)

A user asks to analyze eQTL data and colocalize with a GWAS locus. The planned surface quantifies expression, harmonizes genotypes, maps cis-eQTLs, tests allelic imbalance, and colocalizes. Until skills land, requests degrade to the pubmed + chembl + open-targets MCP fallback.

Validation & benchmarks

Benchmarks

• Planned: permutation-based QTL FDR calibration

Reproducibility. Planned: provenance.json will pin reference panel and mapping window.

Reference

MCP fallback servers (used when the plugin is unavailable): pubmed, chembl, open-targets

Source documents

• DomainOS registry: references/domain-os-registry.md

Composition

Platform opt-in

QTLos runs standalone. When composed under the Hordago platform it gains cross-domain routing, the Shared Compiler gate, and evidence-audit provenance enforcement. Platform composition is opt-in; the quickstart above has zero platform dependency.

Cross-domain dependencies

Engine	Relationship
gwas-os	Colocalizes molecular QTLs with GWAS association signals.