Skip to main content
Glama
biocontext-ai

BioContextAI Knowledgebase MCP

Official

bc_get_cell_ontology_terms

Search the Cell Ontology (CL) for standardized cell type terms using a keyword, with options for exact match and result count.

Instructions

Search OLS for Cell Ontology (CL) terms using a controlled vocabulary for cell types.

Returns: dict: Cell ontology terms with cl_terms array containing id, label, definition, synonyms or error message.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sizeNoMaximum number of results to return
cell_typeYesCell type to search for (e.g., 'T cell', 'neuron')
exact_matchNoWhether to perform exact match search

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

No annotations are provided, so the description carries full burden. It mentions using OLS, a controlled vocabulary, and specifies the return structure (dict with cl_terms array). However, it does not discuss error cases or rate limits, which would enhance transparency.

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 very concise: a single sentence stating purpose, followed by a bullet list of return fields. No redundant information, and the purpose is front-loaded.

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 has 3 parameters and an output schema, the description adequately covers purpose, source (OLS), and return format. It mentions controlled vocabulary. With output schema present, no need to detail return values further. Could mention search behavior nuances, but sufficient overall.

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%, so the description does not add parameter semantics beyond what the schema provides. The schema descriptions are clear, so the baseline score of 3 is appropriate.

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 Cell Ontology (CL) terms, specifying the controlled vocabulary for cell types. This distinguishes it from sibling tools like bc_search_ontology_terms (which searches all ontologies) and bc_get_term_details (which retrieves specific term details).

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 implicitly indicates use for cell type terms but provides no explicit guidance on when to use vs alternatives (e.g., other ontology search tools). No when-not-to-use or alternative recommendations are given, which is a gap given many sibling tools.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/biocontext-ai/knowledgebase-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server