BioContextAI Knowledgebase MCP

Official

Overview Schema Source Related Servers Discussions Admin

bc_get_uniprot_protein_info

Retrieve protein information from UniProt by providing a protein ID, name, or gene symbol. Optionally specify species and include references.

Instructions

Retrieve protein information from UniProt database. Provide at least one of protein_id, protein_name, or gene_symbol.

Returns: dict: Protein information with accession, proteinDescription, genes, organism, sequence, functions, keywords, references 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_uniprot_protein_info"
  }
}

Input Schema

Name	Required	Description
`species`	No	Taxonomy ID (e.g., '10090') or species name
`protein_id`	No	Protein accession number (e.g., 'P04637')
`gene_symbol`	No	Gene symbol to search for (e.g., 'TP53')
`protein_name`	No	Protein name to search for (e.g., 'P53')
`include_references`	No	Include references and cross-references in response

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

Changed10 schema fields changedv1.0.0Jan 3, 2026

changedInput schema / properties / gene_symbol / description

Previous value: -"The gene symbol to search for (e.g., 'TP53')"New value: +"Gene symbol to search for (e.g., 'TP53')"

removedInput schema / properties / gene_symbol / title
```
Removed value: -"Gene Symbol"
```

changedInput schema / properties / include_references / description

Previous value: -"Whether to include references and cross-references in the response"New value: +"Include references and cross-references in response"

removedInput schema / properties / include_references / title
```
Removed value: -"Include References"
```

changedInput schema / properties / protein_id / description

Previous value: -"The protein identifier or accession number (e.g., 'P04637')"New value: +"Protein accession number (e.g., 'P04637')"

removedInput schema / properties / protein_id / title
```
Removed value: -"Protein Id"
```

changedInput schema / properties / protein_name / description

Previous value: -"The name of the protein to search for (e.g., 'P53')"New value: +"Protein name to search for (e.g., 'P53')"

removedInput schema / properties / protein_name / title
```
Removed value: -"Protein Name"
```

changedInput schema / properties / species / description

Previous value: -"Taxonomy ID (e.g., 10090) or species name as string"New value: +"Taxonomy ID (e.g., '10090') or species name"

removedInput schema / properties / species / title
```
Removed value: -"Species"
```

First observedAug 18, 2025

TDQS

A4/5.0

Behavior3/5

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

No annotations are provided, so the description carries the full burden. It discloses the return type (dict with listed fields) and mentions possible error messages, but does not state whether the operation is read-only, requires authentication, or how it handles missing data. Acceptable for a retrieval tool but could be more explicit.

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?

Description is extremely concise: two sentences plus a returns line. No redundant information. Every sentence serves a purpose, and the key constraint is front-loaded. Ideal length for quick understanding.

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 presence of an output schema (context signal), the description does not need to fully explain return values, but it still lists key fields. However, it could mention the usage of the 'species' parameter to narrow results. Overall, adequate for the tool's complexity.

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

Parameters4/5

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

Schema description coverage is 100% (all 5 parameters have descriptions). The description adds value by specifying that at least one of protein_id, protein_name, or gene_symbol must be provided, which is not enforced by the schema (all optional). This helps the agent understand the constraint.

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?

Description clearly states the action ('Retrieve protein information') and the resource ('UniProt database'). It specifies the key parameters (protein_id, protein_name, gene_symbol) and differentiates from sibling tools like bc_get_uniprot_id_by_protein_symbol by focusing on full info retrieval.

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?

Description advises 'Provide at least one of protein_id, protein_name, or gene_symbol', which is a usage constraint. However, it does not explicitly compare to sibling tools or state when to use this tool versus alternatives (e.g., bc_get_protein_domains, bc_get_human_protein_atlas_info).

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

Deploy Server