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BioContextAI Knowledgebase MCP

BioContextAI Knowledgebase MCP

Official
by biocontext-ai
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

bc_get_go_terms_by_gene

Find Gene Ontology terms linked to a gene name, returning IDs, labels, and descriptions from OLS vocabularies.

Instructions

Search OLS for Gene Ontology (GO) terms related to a gene name using structured vocabularies.

Returns: dict: GO terms with go_terms array containing id, label, description, type or error message.

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": {
      "gene_name": "<gene_name>"
    },
    "name": "bc_get_go_terms_by_gene"
  }
}

Input Schema

NameRequiredDescriptionDefault
sizeNoMaximum number of results to return
gene_nameYesGene name or symbol to search for (e.g., 'TP53', 'BRCA1')
exact_matchNoWhether to perform exact match search

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed6 schema fields changedv1.0.0
    • changedInput schema / properties / exact_match / description
      Previous value: -"Whether to perform an exact match search"New value: +"Whether to perform exact match search"
    • removedInput schema / properties / exact_match / title
      Removed value: -"Exact Match"
    • changedInput schema / properties / gene_name / description
      Previous value: -"The gene name or symbol to search for (e.g., 'TP53', 'BRCA1')"New value: +"Gene name or symbol to search for (e.g., 'TP53', 'BRCA1')"
    • removedInput schema / properties / gene_name / title
      Removed value: -"Gene Name"
    • changedInput schema / properties / size / description
      Previous value: -"The maximum number of results to return"New value: +"Maximum number of results to return"
    • removedInput schema / properties / size / title
      Removed value: -"Size"
  2. First observed

TDQS

A3.6/5.0
Behavior2/5

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

With no annotations provided, the description should disclose behavioral traits like idempotency or authorization needs. It only describes return format, lacking context on side effects, rate limits, or safety.

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?

The description is two sentences: purpose and return format. No wasted words, front-loaded, and efficient for rapid scanning.

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

Completeness4/5

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

Given the tool's simplicity (3 params, output schema exists), the description covers key aspects. However, the return description could be more detailed about error cases or pagination.

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 coverage is 100% with each parameter described. The description adds marginal value beyond schema (e.g., example gene names) but does not significantly deepen understanding.

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?

The description clearly states it searches OLS for GO terms related to a gene name, using structured vocabularies. It is specific and distinguishes from sibling tools like search_ontology_terms.

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

Usage Guidelines3/5

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

The description implies usage for GO term lookups but does not explicitly state when to use this tool versus alternatives like bc_search_ontology_terms or provide exclusion criteria.

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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