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yeyuan98

BioMCP

by yeyuan98
OverviewSchemaSourceRelated ServersDiscussionsAdmin
TypeScript
Remote

gene_search

Read-only

Search genes by symbol, name, or keyword to find matching genomic records. Filter results by chromosome and paginate to locate the right gene for variant, disease, or drug research.

Instructions

Search for genes by symbol, name, or keyword

Input Schema

NameRequiredDescriptionDefault
limitNoMaximum results
queryYesGene symbol, name, or keyword to search for
offsetNoResult offset
chromosomeNoFilter by chromosome: 1-22, X, Y, or M/MT (mitochondrial), with an optional "chr" prefix (e.g., "7", "chrX")

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
    • addedInput schema / properties / offset / maximum
      Added value: +9007199254740991
  2. Changed1 schema field changedv1.6.0-alpha.2
    • changedInput schema / properties / chromosome / description
      Previous value: -"Filter by chromosome (e.g., \"7\", \"X\")"New value: +"Filter by chromosome: 1-22, X, Y, or M/MT (mitochondrial), with an optional \"chr\" prefix (e.g., \"7\", \"chrX\")"
  3. Changed1 schema field changedv1.6.0-alpha.1
    • addedInput schema / properties / query / minLength
      Added value: +1
  4. Changed1 schema field changedv0.7.1
    • removedInput schema / properties / gene_type
      Removed value: -{
-  "description": "Filter by gene type",
-  "enum": [
-    "protein-coding",
-    "ncRNA",
-    "pseudo"
-  ],
-  "type": "string"
-}
  5. First observedv0.1.8

TDQS

C2.9/5.0
Behavior2/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so safety and scope are covered externally. The description adds nothing beyond those hints — no note on matching behavior (fuzzy vs exact symbol match), result ordering, or how to page through large hit sets.

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

Conciseness4/5

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

One compact sentence with the resource and match criteria front-loaded and no filler. It is appropriately sized, though its brevity edges into under-specification rather than pure efficiency.

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

Completeness3/5

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

For a simple read-only search with 100% schema coverage and no output schema, the definition is minimally sufficient to call the tool. It still omits result shape, whether paging is expected, and how matches are ranked, so an agent gets no help interpreting the response.

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

Parameters3/5

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

Schema description coverage is 100%, so all four parameters (query, chromosome, limit, offset) are already documented in the schema, and that sets the baseline at 3. The description only echoes the query parameter's three modes and ignores the chromosome filter, limit, and offset, adding no extra meaning.

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

Purpose4/5

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

States a specific verb (search) and resource (genes) plus the match fields (symbol, name, keyword), so the operation is unambiguous. It does not distinguish itself from siblings like gene_get or gene_diseases, leaving the search-vs-lookup split to inference from the names.

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

Usage Guidelines2/5

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

The description says what can be searched but never when to pick this over gene_get (exact retrieval) or gene_enrich (set-based analysis). An agent must infer from the tool names that search is for discovery when no identifier is known.

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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