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Disease

Use disease commands for normalization and disease-centric cross-entity pivots.

Search diseases

biomcp search disease -q melanoma --limit 5
biomcp search disease -q glioblastoma --source mondo --limit 5

Search resolves common labels toward canonical ontology-backed identifiers.

Get disease records

By label:

biomcp get disease melanoma

By MONDO identifier:

biomcp get disease MONDO:0005105

Disease sections

Genes (Monarch-backed associations with relationship/source when available):

biomcp get disease MONDO:0005105 genes

Phenotypes (HPO phenotypes with qualifiers):

biomcp get disease MONDO:0005105 phenotypes

Variants (Monarch disease-associated variants):

biomcp get disease MONDO:0005105 variants

Models (Monarch model-organism evidence):

biomcp get disease MONDO:0005105 models

Combined sections:

biomcp get disease MONDO:0005105 genes phenotypes variants models
biomcp get disease MONDO:0005105 all

Use HPO term sets for ranked disease candidates:

biomcp search phenotype "HP:0001250 HP:0001263" --limit 10

You can pass terms space-separated or comma-separated.

Typical disease-centric workflow

  1. Normalize disease label.
  2. Pull disease sections (genes, phenotypes, variants, models) for context.
  3. Use normalized concept for trial or article searches.

Example:

biomcp get disease MONDO:0005105 genes phenotypes
biomcp search trial -c melanoma --status recruiting --limit 5
biomcp search article -d melanoma --limit 5

JSON mode

biomcp --json get disease MONDO:0005105 all
biomcp --json search phenotype "HP:0001250 HP:0001263"

Practical tips

  • Prefer MONDO IDs in automation workflows.
  • Keep raw labels in user-facing notes for readability.
  • Pair disease normalization with biomarker filters for trial matching.