GEOmend

GEOmend combines metadata from GEO studies and local tables. Start with one project: add datasets → inspect suggestions → refine or review → export. Source artifacts, fixed review evidence, decisions, and output history are retained.

Start

Python 3.13+ is required. The default install includes standard workflow dependencies.

python -m pip install geomend
geomend project create samples-a.tsv samples-b.tsv --project my-project
geomend project summary my-project
geomend project tasks my-project --json
geomend project exports plan my-project --mode best_guess --json
geomend project exports table my-project --mode best_guess --output metadata.tsv --profile analysis

Inputs can be GEO accessions, family-SOFT files, or CSV/TSV metadata. Initial suggestions and best_guess output are provisional. Choose --mode reviewed explicitly for a cohort table restricted to reviewed mappings. Review and transformation completeness do not prove source meaning.

Python and browser clients

from geomend.project import ProjectClient

project = ProjectClient.open("my-project")
summary = project.summary()
work = project.tasks(limit=20)
fields = project.mappings.fields(limit=20)
plan = project.exports.plan(mode="best_guess")
project.exports.table("metadata.csv", mode="best_guess", expected_plan_sha256=plan.plan_sha256)

The starting interface has create, open, summary, tasks, and capabilities. Expand inputs, mappings, concepts, transformations, review, exports, or administration when needed. Discovery and navigation are read-only; they never accept suggestions, refresh reviews, or materialize output.

Use geomend project administration serve my-project for the authenticated loopback service under /api/v1. Download its browser client, which exposes the same starting and domain operations. GUI clients own presentation and drafts; GEOmend owns scientific decisions and their validation.

Review with others

geomend project review assign my-project --output-dir round-one --reviewer a --reviewer b --json

Reviewers use geomend.reviewer.ReviewerClient or the portable review CLI to inspect fixed evidence, preview judgments, and save responses. Import responses with project review import, compare with project review compare, and issue synthesis with project review synthesize. Round IDs identify the original issuer. Review hierarchy organizes work without weighting reviewers by title.

See the two project journeys, reviewer protocol, and advanced reference. geomend project --help shows domains; geomend project --expanded-help shows every option.

Advanced workflows

Standalone reconciliation supports curated registries and immutable reviewed workspaces through geomend reconcile plan followed by geomend reconcile run. Native data and audit exports retain distinct contracts. Ontology, transformation, identity, snapshot, fork, and storage operations remain available through focused interfaces. Never edit review SQLite or response records directly.

Learned retrieval adds dependencies through geomend[learned]. Local Ollama is optional and never downloaded automatically. Training and scientific benchmarks live in geomend-research; see the development boundary.

For checkout development, use the existing environment from the repository root:

PYTHONPATH="$PWD/src" .venv/bin/geomend capabilities --json

Source artifacts remain immutable. Suggestions, reviewer preferences, effective mappings, and export readiness are distinct states. Scores rank evidence; they are not probabilities of correctness. GEOmend does not infer scientific equivalence from matching strings or deduplicate samples across studies automatically.