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BioContextAI Knowledgebase MCP

BioContextAI Knowledgebase MCP

Official
by biocontext-ai
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Hybrid

bc_get_protein_domains

Retrieve protein domain architecture and InterPro functional site matches. Enter a UniProt ID to get domain structure, match count, and optional structural data.

Instructions

Get protein domain architecture and InterPro matches. Returns all InterPro domains, functional sites, and domain architecture.

Returns: dict: Protein metadata with interpro_matches array, interpro_match_count, domain_architecture, optionally structure data 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": {
      "protein_id": "<protein_id>"
    },
    "name": "bc_get_protein_domains"
  }
}

Input Schema

NameRequiredDescriptionDefault
source_dbNoDatabase source ('uniprot', 'reviewed', or 'unreviewed')uniprot
protein_idYesUniProt ID/accession (e.g., 'P04637' or 'CYC_HUMAN')
species_filterNoTaxonomy ID filter (e.g., '9606' for human)
include_structure_infoNoInclude structural information

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed8 schema fields changedv1.0.0
    • changedInput schema / properties / include_structure_info / description
      Previous value: -"Whether to include structural information"New value: +"Include structural information"
    • removedInput schema / properties / include_structure_info / title
      Removed value: -"Include Structure Info"
    • changedInput schema / properties / protein_id / description
      Previous value: -"The protein identifier/accession (e.g., 'P04637' or 'CYC_HUMAN')"New value: +"UniProt ID/accession (e.g., 'P04637' or 'CYC_HUMAN')"
    • removedInput schema / properties / protein_id / title
      Removed value: -"Protein Id"
    • changedInput schema / properties / source_db / description
      Previous value: -"The protein database source ('uniprot', 'reviewed', or 'unreviewed')"New value: +"Database source ('uniprot', 'reviewed', or 'unreviewed')"
    • removedInput schema / properties / source_db / title
      Removed value: -"Source Db"
    • changedInput schema / properties / species_filter / description
      Previous value: -"Taxonomy ID to filter results (e.g., '9606' for human)"New value: +"Taxonomy ID filter (e.g., '9606' for human)"
    • removedInput schema / properties / species_filter / title
      Removed value: -"Species Filter"
  2. First observed

TDQS

A3.6/5.0
Behavior3/5

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

No annotations are provided, so the description carries full burden. It discloses return format (dict with interpro_matches, domain_architecture, optionally structure data) but lacks details on performance, rate limits, or side effects. The read-only nature is implied but not 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?

The description is two sentences plus a return format snippet, providing essential information without unnecessary words. Information is front-loaded with the purpose.

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 full schema coverage and the presence of an output schema, the description adequately explains the tool's function and return structure. However, it could be more complete by explaining how it differs from related protein tools.

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?

All 4 parameters are described in the input schema (100% coverage). The description adds no additional meaning beyond reiterating that protein_id is required. 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 retrieves protein domain architecture and InterPro matches, specifying the output includes interpro_matches, functional sites, and domain architecture. This distinguishes it from sibling tools like bc_get_uniprot_protein_info or bc_get_interpro_entry by focusing on domain architecture.

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

Usage Guidelines2/5

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

No guidance is provided on when to use this tool versus alternatives (e.g., bc_get_interpro_entry or bc_get_uniprot_protein_info). The description only states what it does, not context for selection.

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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