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Biology Skills

Skills

Biology Skills uses a small number of broad domain skills so AI agents can activate the relevant biological guidance reliably.

Each domain contains:

  • SKILL.md for cross-cutting rules and routing
  • references/ for focused expert guidance on individual biological or computational topics

Available skills

biology-core

Foundational biological reasoning that applies across domains.

Covers:

  • biological and experimental context
  • evidence and claim strength
  • observation versus prediction and inference
  • association, mechanism, and causality
  • identifiers, versions, and provenance
  • ambiguity and interpretation boundaries

Use biology-core whenever omitted context, provenance, evidence type, or inference level could materially change a biological conclusion.

genomics

Biological and computational correctness for genomic data, analysis, interpretation, and reporting.

Covers:

  • genome organisation
  • reference genomes and exact reference identity
  • FASTA and reference sequence files
  • FASTQ and sequencing quality
  • SAM, BAM, CRAM, and alignment indexes
  • genomic intervals and coordinate conventions
  • VCF, BCF, gVCF, and variant indexes
  • variant representation and normalisation
  • HGVS variant nomenclature
  • transcripts and isoforms
  • coding and protein consequences
  • inheritance, phase, segregation, and mosaicism
  • gene expression and regulatory context

Use genomics whenever reference sequences, coordinates, file semantics, variants, transcripts, genotypes, inheritance, or genomic interpretation affect correctness.

Using skills together

biology-core provides the general foundation. Domain skills add the rules specific to a field.

For example, a variant-interpretation task may require both:

biology-core
  → What does the evidence justify claiming?

genomics
  → What reference, allele, transcript, phase, and nomenclature define the result?

Agents should load only the relevant detailed references for the task rather than treating every topic page as required context.

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