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How to: orient with search all

search all is the counts-first orientation command for cross-entity work. Use it when you know the biomedical concept you care about but do not yet know which BioMCP entity is the best next stop.

It fans out across relevant sections based on the slots you provide, then helps you choose a narrower follow-up command.

Start with typed slots

Named slots are the primary contract because they make your intent explicit:

biomcp search all --gene BRAF --disease melanoma
biomcp search all --drug pembrolizumab
biomcp search all --variant "BRAF V600E"
biomcp search all --keyword "checkpoint inhibitor"

Short flags are equivalent where supported:

biomcp search all -g BRAF -d melanoma
biomcp search all -v "BRAF V600E"
biomcp search all -k "checkpoint inhibitor"

Use --counts-only for a low-noise orientation pass

--counts-only keeps the section totals and next-step links while suppressing row tables. That makes it easier to decide which entity to inspect next.

biomcp search all --gene BRAF --counts-only
biomcp search all --gene BRAF --disease melanoma --counts-only
biomcp search all --drug pembrolizumab --counts-only

In markdown output, each section keeps its heading and shows the stable marker Rows omitted (`--counts-only`).

Narrow the next command intentionally

After the orientation pass, move to the entity that best matches your question:

# Trial follow-up after gene+disease orientation
biomcp search trial -c melanoma --biomarker BRAF --status recruiting --limit 5

# Article follow-up after orientation reveals literature volume
biomcp search article -g BRAF -d melanoma --date-from 2024-01-01 --limit 5

# Helper pivots when you already know the anchor entity
biomcp gene trials BRAF
biomcp variant trials "BRAF V600E" --limit 5

Positional compatibility syntax

The positional form is supported only as a compatibility alias for --keyword:

biomcp search all BRAF
biomcp search all --keyword BRAF

Prefer named slots in new docs, scripts, and demos. They are the primary teaching path and avoid ambiguity about whether a term is a gene, disease, drug, variant, or general keyword.