omics-target-evidence-mapper

Why This Exists

Researchers often need a quick first-pass view of whether a gene or protein target has evidence across multiple public sources. In practice, this usually means checking several websites manually and informally combining results. This skill makes that process reproducible by retrieving and organising public evidence into one structured output.

This skill is for research triage only. It does not infer causality, rank therapeutic value, or make clinical recommendations.

Core Capabilities

1. Accept a gene or protein target and an optional disease term.
2. Retrieve canonical target information from UniProt.
3. Retrieve disease-target association evidence from Open Targets.
4. Retrieve recent literature hits from PubMed.
5. Optionally retrieve trial records relevant to the target and disease.
6. Produce a machine-readable JSON file and a human-readable Markdown report.

Input Formats

Argument	Required	Example	Notes
--gene	Yes, unless --demo is used	IL6R	Gene or target symbol
--disease	No	coronary artery disease	Optional disease context
--output	Yes	demo_out	Output directory
--max-papers	No	5	Number of PubMed hits to include
--max-trials	No	5	Number of trial records to include
--demo	No	--demo	Runs the built-in demo query

Workflow

1. Validate CLI inputs.
2. Resolve the query from either user input or demo mode.
3. Query public data sources.
4. Normalise results into a structured evidence object.
5. Write JSON and Markdown outputs.
6. Write reproducibility bundle:
   • reproducibility/checksums.sha256 — SHA-256 hashes of all output files
   • reproducibility/environment.yml — pinned Conda/pip environment
   • ro-crate-metadata.json — RO-Crate 1.1 provenance record (run params, outputs, script)

CLI Reference

Demo mode

python skills/omics-target-evidence-mapper/omics_target_evidence_mapper.py --demo --output demo_out