BioBTree

biobtree_variant

Sugi Variant reference for one specific small variant or structural variant (built from ClinVar, AlphaMissense and dbVar data).

SYNTAX: biobtree_variant(entities=["PTEN R130Q"])

CALL for a specific change: its classification, review status, rsID, coordinate, transcript/HGVS identity, computational & population evidence, associated conditions, or the dbVar record for a structural variant. Cite the returned canonical_url.

Resolution keys: slug, rsID, GRCh38 coordinate (10:87933148:G:A), GENE + HGVS ("PTEN R130Q"), ClinVar VCV..., dbVar NSSV.../nsv..., exact SV coordinate, or a locus chr:start-end.
A single hit returns a digest (Summary + Identity) and the page's sections; pass section="Identity" (a name from sections) for one zone, or full=true for the whole page.
If ambiguous is true, do not guess and do not summarize all candidates as if they were one variant; pass slug= or gene= to disambiguate, or ask the user which change they mean. include="digests" returns Summary+Identity for up to five candidates, still marked ambiguous.
Use biobtree_map / biobtree_entry for identifier mappings or per-dataset records; use biobtree_atlas for gene/disease/drug overviews.

RETURNS: results [{entity, kind, slug, canonical_url, release, content, sections}], ambiguous [{query, hits, note}], not_found, fetch_errors

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "entities": "<entities>"
    },
    "name": "biobtree_variant"
  }
}

Input Schema

Name	Required	Description
`full`	No	Return the entire page (large; avoid for multiple entities)
`gene`	No	Optional gene symbol to disambiguate a multi-hit query
`slug`	No	Exact variant page slug
`include`	No	For ambiguous multi-hit results only: return a digest for up to five candidates
`section`	No	Return one section instead of the digest; use a name from the result's `sections` (e.g. 'Identity')
`entities`	Yes	Variant keys: slug, rsID, GRCh38 coordinate, GENE+HGVS, VCV/NSSV id, or locus chr:start-end

Schema Changelog

Changes observed during successful MCP inspections.

AddedNov 8, 2026

TDQS

A4.7/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full behavioral burden and does so well: single-hit digest composition (Summary + Identity + `sections`), `full=true` returning a large whole page, `include="digests"` capping candidates at five while remaining flagged ambiguous, and the result envelope (results/ambiguous/not_found/fetch_errors). It does not cover auth, rate limits, or cost of repeated calls beyond the 'large; avoid for multiple entities' warning.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded one-line purpose, then labeled blocks (SYNTAX, CALL, resolution keys, disambiguation, alternatives, RETURNS). Dense but every line carries actionable information; no restatement of the title or filler.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

No output schema exists, and the description compensates by spelling out the return envelope and the digest-vs-section-vs-full modes. All six parameters are covered, and the ambiguity path — the highest-risk failure mode for this tool — is fully specified.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline would be 3, but the description adds genuine meaning: it enumerates the accepted resolution keys (slug, rsID, GRCh38 coordinate form '10:87933148:G:A', GENE+HGVS, VCV, NSSV/nsv, locus), explains that `section` must be a name taken from the result's `sections`, and ties `slug`/`gene` to the disambiguation flow rather than leaving them as bare strings.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific resource and scope: a reference page for one specific small variant or structural variant, built from named sources (ClinVar, AlphaMissense, dbVar). The final paragraph explicitly distinguishes it from biobtree_map/biobtree_entry (identifier mappings, per-dataset records) and biobtree_atlas (gene/disease/drug overviews).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives a concrete CALL trigger ('classification, review status, rsID, coordinate, transcript/HGVS identity...'), names the sibling tools and the conditions that select them, and states an explicit when-not: if `ambiguous` is true, do not guess and do not summarize candidates as one variant.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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