Labcoat entity discipline

Skill qchiujunhao/labcoat/skills/labcoat-entity-discipline

Skills, hooks, and CLI checks for safer biomedical AI coding agents.

Install

npx -y skills add qchiujunhao/labcoat --skill labcoat-entity-discipline

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Gene, variant, disease, drug, protein, cell type, tissue, marker, ortholog, HGVS, rsID, transcript, species, and genome-build ambiguity discipline. Use when biomedical entity interpretation could change by organism, identifier system, reference, or provenance.

SKILL.md

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Entity Discipline

Biomedical names are not universal. Require enough context before interpreting them.

Decision Ladder

Identify entity type: gene, variant, disease, drug, protein, tissue, cell type, pathway, sample, coordinate.
Require organism/species for gene symbols and markers.
Require genome build for genomic coordinates and VCF/BED/BAM/GTF/GFF/liftOver work.
Require transcript/reference sequence for HGVS or protein-change claims.
Use stable identifiers where possible; preserve user-provided uncertainty.

Allowed

Ask for missing species, build, transcript, or identifier source.
Flag ambiguous marker panels and aliases.
Use scripts/detect_bio_entities.py for a quick deterministic entity scan.

Disallowed

Do not infer human because symbols are uppercase.
Do not infer GRCh38/hg38 because coordinates look modern.
Do not invent clinical significance, citation, or variant interpretation.

Output

Use:

Entity:
Missing context:
Risk:
Minimal safe next step:

Read references/entity-ambiguity.md for common ambiguity patterns.