dismech: Skill for Claude Code

Curate a Disease Grouping

Treat kb/groupings/ as the source of truth. A grouping is an explicit curated union of already-distinct diseases, modules, or other groupings. It validates against Grouping, not Disease, and points down by listing members; it does not recreate the MONDO hierarchy.

Discover relevant examples

rg --files kb/groupings -g "*.yaml" | sort
rg -il "<disease family or mechanism>" kb/groupings
sed -n "1,160p" kb/groupings/Mucopolysaccharidoses.yaml

Use Mucopolysaccharidoses for a NECESSARY criteria example and Inherited_Arrhythmia_Syndromes for nested boolean logic with NECESSARY_AND_SUFFICIENT criteria. Inspect the current YAML rather than copying a static catalog.

Define the boundary

• Set name, optional display_name, creation_date, description, grouping_basis, grouping_rationale, membership_criteria, and members.
• Use grouping_basis to record why the members belong together; inspect the schema for current enum values rather than inventing one.
• Explain the lump/keep-split boundary in grouping_rationale. A grouping sits over distinct entities, so do not put a LUMP flag on it.
• An optional MONDO mapping is a cross-reference, not the source of membership.

Model membership criteria

Each membership_criteria block needs a human-readable description. Its optional logic is a LogicalCriterion tree:

• Branch nodes use operator: AND, OR, or NOT with operands.
• Leaf nodes use criterion_predicate and the matching payload: HAS_PHENOTYPE, HAS_GENE, CONFORMS_TO_MODULE, HAS_BIOLOGICAL_PROCESS, HAS_MOLECULAR_FUNCTION, HAS_CLASSIFICATION, HAS_INHERITANCE, HAS_MAPPING, or OTHER. Channelopathies is the worked HAS_MOLECULAR_FUNCTION example: a NECESSARY GO activity criterion alongside a NECESSARY_AND_SUFFICIENT classification-tag criterion. A HAS_MOLECULAR_FUNCTION criterion checks the GO terms each entry curates, not the GO annotations of its causal genes. After adding or editing one, run just grouping-gene-go-audit --grouping <name> (network, report-only) to see whether each member's causal genes carry the activity, either in GO's annotations or as a core function in their ai-gene-review review. An UNSUPPORTED member is a lead: the member may not belong, its gene may not be reviewed yet, or the activity may sit on another gene.
• Use negated: true to negate a leaf when clearer than a NOT branch.