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BioContextAI Knowledgebase MCP

BioContextAI Knowledgebase MCP

Official
by biocontext-ai
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

bc_get_panglaodb_options

Retrieve unique organ and cell type values from the PanglaoDB dataset to filter marker gene searches.

Instructions

Retrieve available filter options for PanglaoDB marker genes. Returns unique values for organs and cell types.

Returns: dict: Lists of unique organ and cell_type values available in PanglaoDB dataset or error message.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "bc_get_panglaodb_options"
  }
}

Input Schema

NameRequiredDescriptionDefault

No arguments

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.9/5.0
Behavior3/5

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

With no annotations, the description must fully disclose behavior. It states it returns a dict or error message, which is adequate for a simple retrieval tool with no parameters. However, it does not mention side effects, authentication needs, or rate limits, which are likely not applicable but not explicitly stated.

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: the first sentence states the purpose, the second describes the return value. No unnecessary words, front-loaded, and easy to parse.

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?

Given the tool has zero parameters, an output schema, and a straightforward purpose, the description fully covers its functionality. The return type and source (PanglaoDB dataset) are mentioned, making it complete for selection and invocation.

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?

There are no parameters, and schema coverage is 100% (vacuous). Per rules, baseline is 3. The description adds no parameter information because none is needed.

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 states the verb 'Retrieve' and resource 'available filter options for PanglaoDB marker genes', and specifies the return values 'organs and cell types'. It is specific and clearly distinguishes from sibling tools like bc_get_panglaodb_marker_genes.

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 the tool provides filter options, likely for use before querying marker genes, but does not explicitly state when to use it versus alternatives such as bc_get_panglaodb_marker_genes. No direct usage or exclusion instructions are given.

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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