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Labcoat entity discipline

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

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.From its SKILL.md

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

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

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SKILL.md

1.4 KB, 235 tokens by cl100k_base, as published. Nobody here has run it

Entity Discipline

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

Decision Ladder

  1. Identify entity type: gene, variant, disease, drug, protein, tissue, cell type, pathway, sample, coordinate.
  2. Require organism/species for gene symbols and markers.
  3. Require genome build for genomic coordinates and VCF/BED/BAM/GTF/GFF/liftOver work.
  4. Require transcript/reference sequence for HGVS or protein-change claims.
  5. 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.

What ships with it: 2 files

1.3 KB alongside SKILL.md, 1 of them executable

references/

scripts/

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