name: biomcp description: Search and retrieve biomedical data - genes, variants, clinical trials, diagnostic tests, articles, drugs, diseases, pathways, proteins, adverse events, pharmacogenomics, and phenotype-disease matching. Use for gene function, variant pathogenicity, trials, diagnostics, drug safety, pathway context, disease workups, and literature evidence.

BioMCP CLI

If you don't know how to start, run biomcp skill list first, then open the matching biomcp skill <slug> playbook for the full workflow.

Routing rules

• Start with the narrowest command that matches the question.
• Use biomcp discover "<free text>" when you only have a single biomedical phrase and need the CLI to resolve the first typed command. discover is a single-entity resolver and single-entity free-text lookup only: use it to resolve the canonical name, ID, or category of one thing. It is not a relational query tool and not a list-question seed. Examples: biomcp discover BRCA1 and biomcp discover dabigatran. Symptom-of-disease prompts, HPO symptom bridges, treatment prompts, gene+disease orientation, and unambiguous gene-plus-topic follow-ups remain supported exceptions.
• Relational or multi-entity questions may redirect to biomcp search all --keyword "<query>" instead of surfacing weak collocation matches as if they were a resolved discover answer.
• Use biomcp search all --gene <gene> --disease "<disease>" when you know the entities but not the next pivot.
• Treatment questions: biomcp search drug --indication "<disease>" --limit 5
• Diagnostic-test questions: use structured pivots first with biomcp get gene <symbol> diagnostics or biomcp get disease "<disease>" diagnostics; use biomcp list diagnostic for the full source/filter/section contract; use biomcp search diagnostic --gene <symbol> --limit 5, biomcp search diagnostic --disease "<disease>" --source all --limit 5, or biomcp get diagnostic <id> when you need the full search/detail surface.
• Symptom or phenotype questions: biomcp get disease <name_or_id> phenotypes
• Gene-function questions: biomcp get gene <symbol>
• Drug-safety questions: biomcp drug adverse-events <name> and biomcp get drug <name> safety
• Drug-interaction questions: biomcp drug interactions <name> and biomcp get drug <name> interactions
• EMA and WHO regional drug data are local runtime files that auto-download on first use, DDInter is the local drug-interaction bundle, CDC CVX/MVX is the companion local vaccine-brand bridge for default/EU vaccine searches plus explicit WHO vaccine search, and GTR plus WHO IVD are local diagnostic-test backbones; run biomcp ddinter sync, biomcp ema sync, biomcp who sync, biomcp cvx sync, biomcp gtr sync, or biomcp who-ivd sync to force-refresh before freshness-sensitive local-runtime lookups.
• Vaccine brand-name questions that miss on MyChem often need biomcp search drug <brand> --region eu, omitted --region, or explicit biomcp search drug <brand> --region who --product-type vaccine, which can bridge through CDC CVX/MVX into EMA or WHO vaccine matches.
• Review-literature questions: biomcp search article -k "<query>" --type review --limit 5
• Exact gene-plus-protein literature questions: resolve/check identity, then use biomcp variant articles "MSH2 p.L341P" --limit 5; an ordinary search article -k "MSH2 p.L341P" remains unchanged but may suggest that helper in _meta.next_commands.
• Article-search JSON is compact by default; use --full only when abstracts, full provenance, or ranking diagnostics are needed. --sort date replaces relevance ranking, so preserve and heed _meta.warnings[].
• Keyword-only article searches may return _meta.suggestions[] objects when the whole keyword exactly matches a gene, drug, or disease label/alias; use the suggested get gene, get drug, or get disease command when structured data may answer before more article paging.
• For repeated article keyword searches in one task, use JSON plus --session <token> with a short non-secret local label. If the next keyword overlaps the previous same-session keyword, _meta.suggestions[] can point to prior article batch, discover, or date narrowing instead of more reformulation.
• Some first-call JSON responses include _meta.workflow and _meta.ladder[]; these are static sidecar-backed multi-step ladders. Treat _meta.next_commands as dynamic one-hop follow-ups and _meta.ladder[] as the worked-example path for the named workflow.
• After search article, default to biomcp article batch <id1> <id2> ... instead of repeated get article calls. Batch up to 20 shortlisted papers in one call.
• Use biomcp batch gene <GENE1,GENE2,...> when you need the same basic card fields, chromosome, or sectioned output for multiple genes.
• For diseases with weak ontology-name coverage, run biomcp discover "<disease>" first, then pass a resolved MESH:..., OMIM:..., ICD10CM:..., MONDO:..., or DOID:... identifier to biomcp get disease.
• Multi-hop article follow-up: biomcp article citations <id> --limit 5 and biomcp article recommendations <id> --limit 5

Section reference

• get gene ... protein: UniProt function and localization detail
• get gene ... hpa: Human Protein Atlas tissue expression and localization
• get gene ... expression: GTEx tissue expression
• get gene ... diseases: disease associations
• get gene ... diagnostics: GTR diagnostic-test pivot for a gene
• get article ... annotations: PubTator normalized entity mentions for standardized extraction
• get article ... tldr: Semantic Scholar summary and influence
• get disease ... genes: associated genes
• get disease ... phenotypes: HPO phenotype annotations; source-backed and sometimes incomplete
• get disease ... pathways: pathways from associated genes
• get disease ... diagnostics: GTR and WHO IVD diagnostic-test pivot for a condition
• get diagnostic ... genes: joined gene names from the GTR detail bundle
• get diagnostic ... conditions: joined disease or condition names from GTR
• get diagnostic ... methods: source-native GTR testing methods
• get diagnostic ... regulatory: opt-in FDA device 510(k) and PMA overlay for supported diagnostic records
• get drug ... label: FDA label indications, warnings, and dosage
• get drug ... regulatory: regulatory summary
• get drug ... safety: safety context and warnings
• get drug ... interactions: DDInter-backed structured drug-drug interactions plus source-scoped empty wording
• get drug ... targets: ChEMBL and OpenTargets targets
• get drug ... indications: OpenTargets indication evidence

Cross-entity pivot rules

• gene articles <symbol> and search article -g <symbol> are equivalent starting points for gene-filtered literature.
• Use helpers when the pivot is obvious: drug interactions, drug trials, disease trials, variant articles, article citations.
• Use sectioned diagnostic pivots for gene or disease contexts: get gene <symbol> diagnostics and get disease <name_or_id> diagnostics. Use biomcp list diagnostic for source/filter/section details, and inspect returned IDs with get diagnostic <id> rather than inventing accessions or product codes.
• Use search article -d "<disease>" --type review --limit 5 when disease phenotypes or drug indications look sparse.
• Use article batch as the default multi-article follow-up after search article; it replaces sequential get article calls and preserves Semantic Scholar enrichment when available.
• Use batch <entity> <id1,id2,...> --sections <s1,s2,...> when you need the same card shape for several entities.
• Use enrich <GENE1,GENE2,...> once you have a real gene set and want pathways or GO-style categories.

How-to reference

For question patterns that need more than a one-line routing hint, start with the executable command or routing phrase below before you improvise the command sequence.

| Question pattern | Start with | Why | |---|---|---| | Specific variant pathogenicity or clinical-evidence question | biomcp get variant "<variant>" | Use the bounded variant-pathogenicity workflow instead of mixing ad hoc variant, trial, and article commands | | Exact gene-plus-protein literature retrieval | biomcp skill exact-variant-literature | Resolve strict identity, build the compact union shortlist, batch candidate summaries, then request selected full text/assets and conditionally expand citations/references | | Specific drug safety or adverse-event question | biomcp drug adverse-events <name> and biomcp get drug <name> safety | Start with the drug-safety workflow before widening to literature | | Drug interaction question for a known medication | biomcp drug interactions <name> or biomcp get drug <name> interactions | Start with the DDInter-backed helper when the anchor drug is known, then widen to safety or literature only for nuance | | Drug approval, licensing, or regulatory-date question | biomcp get drug <name> regulatory | Use the structured-first workflow discipline: check get drug ... regulatory before falling back to articles for approval facts | | Broad gene-in-disease orientation | biomcp search all --gene <gene> --disease "<disease>" | Follow the shipped counts-first workflow for gene, drug, trial, and article pivots | | Gene-disease association for a known gene | biomcp get gene <symbol> diseases | Check get gene ... diseases and search variant --gene ... for the full disease spectrum before searching articles | | Gene localization or protein-function question | biomcp get gene <symbol> protein and biomcp get gene <symbol> hpa | Pull get gene ... protein and get gene ... hpa first because UniProt and HPA usually answer localization or function directly | | Diagnostic-test inventory or detail question | biomcp list diagnostic and biomcp get diagnostic GTR000006692.3 | Inspect the shipped diagnostic filters and sections first; use gene/disease diagnostic pivots or search diagnostic to get source-native IDs before get diagnostic detail | | You know the concept but not the first entity to inspect | biomcp search all --keyword "<concept>" | Use search all to choose the next typed command intentionally | | You need to normalize one clinical or guideline term to ontology or clinical codes | biomcp skill normalize-to-codes | Follow the discover workflow for source-labelled MONDO, HPO, ICD-10, SNOMED, or RxNorm-style identifiers | | "Most common" or prevalence question about a disease | biomcp discover "<disease>" | Use biomcp discover to resolve the canonical disease entity, then inspect structured disease data before widening to article search | | You already know the anchor entity and want the built-in related view | Use the matching helper such as biomcp gene articles <symbol>, biomcp drug interactions <name>, biomcp drug trials <name>, or biomcp disease trials "<disease>" | Move from a known gene, disease, drug, or variant into trials, articles, drugs, pathways, or interaction review without rebuilding the query | | You need literature for a known gene, disease, drug, method, or outcome | biomcp search article -k "<query>" --type review --limit 5 | Translate the question into typed flags plus a focused keyword clause | | You need recruiting or completed trials for a disease, drug, or biomarker | biomcp search trial -c "<condition>" --limit 5 | Start with condition and intervention filters, then add biomarker or geography only when needed | | You need to resolve or annotate a variant identifier | biomcp get variant "<variant>" | Normalize the variant first, then add significance or frequency filters | | You need a functional-effect prediction for a variant | biomcp get variant "<variant>" predict | Use predict only after you have a resolvable variant identifier | | You need to reproduce a paper-style workflow | Map the paper task to the closest Bi