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bc_get_panglaodb_marker_genes

Retrieve marker genes from the PanglaoDB dataset, filtering by species, organ, cell type, gene symbol, or sensitivity/specificity scores.

Instructions

Retrieve marker genes from PanglaoDB dataset with optional filters. Supports filtering by species, scores, organ, cell type, gene symbol.

Returns: dict: Markers array with gene symbols, cell types, organs, sensitivity/specificity scores or error message.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
speciesYesSpecies: 'Hs' for Human or 'Mm' for Mouse
min_sensitivityNoMinimum sensitivity score (0-1), applied to species-specific column
min_specificityNoMinimum specificity score (0-1), applied to species-specific column
organNoOrgan filter (e.g., 'Brain', 'Lung'), case-insensitive
cell_typeNoCell type filter (e.g., 'Smooth muscle cells', 'T cells'), case-insensitive
gene_symbolNoGene symbol filter (e.g., 'MAFB', 'SYNPO'), case-insensitive

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior3/5

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

With no annotations, the description must disclose behavioral traits. It specifies the return format (dict with markers array including gene symbols, cell types, organs, scores) and mentions error messages, but does not cover side effects, authentication, rate limits, or pagination. It is adequate but not comprehensive.

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 concise, with a clear first sentence stating the core function, followed by a list of filters and a return description. No unnecessary words, well-structured for quick parsing.

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 6 parameters with optional filters and an output schema, the description covers the return format and filter options well. However, it does not mention behavior when filters yield no results, defaults, or error handling specifics, leaving minor gaps.

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 the description adds little beyond restating the filter types (species, scores, organ, cell type, gene symbol). It does not provide examples or explain relationships between parameters, making it baseline adequate.

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 retrieves marker genes from the PanglaoDB dataset, specifying the data source and optional filters. It distinguishes itself from sibling tools that focus on drugs, proteins, and other biomedical data, leaving no ambiguity about its purpose.

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 retrieving marker genes with filters but does not explicitly state when to use this tool versus alternatives, nor does it provide context on appropriate use cases or limitations. The purpose is clear from sibling names, but explicit guidance is lacking.

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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