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BioContextAI Knowledgebase MCP

BioContextAI Knowledgebase MCP

Official
by biocontext-ai
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Python
Hybrid

bc_search_pride_proteins

Search for proteins identified in a PRIDE mass spectrometry project by accession, name, or keyword. Retrieve protein details including accessions, names, genes, sequences, and modifications from specific proteomics datasets.

Instructions

Search for proteins identified in a specific PRIDE mass spectrometry project. Useful for finding specific proteins in proteomics datasets.

Returns: dict: Proteins list with accessions, names, genes, sequences, modifications, associated projects 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": {
      "project_accession": "<project_accession>"
    },
    "name": "bc_search_pride_proteins"
  }
}

Input Schema

NameRequiredDescriptionDefault
project_accessionYesPRIDE project accession to search proteins in
keywordNoSearch keyword for protein names or accessions
page_sizeNoNumber of results to return (max 100)
sort_fieldNoSort field: accession, proteinName, or geneaccession
sort_directionNoSort direction: ASC or DESCASC

Output Schema

NameRequiredDescriptionDefault

No arguments

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed7 schema fields changedv1.0.0
    • removedInput schema / properties / keyword / title
      Removed value: -"Keyword"
    • removedInput schema / properties / page_size / title
      Removed value: -"Page Size"
    • changedInput schema / properties / project_accession / description
      Previous value: -"The PRIDE project accession to search proteins in"New value: +"PRIDE project accession to search proteins in"
    • removedInput schema / properties / project_accession / title
      Removed value: -"Project Accession"
    • removedInput schema / properties / sort_direction / title
      Removed value: -"Sort Direction"
    • changedInput schema / properties / sort_field / description
      Previous value: -"Field to sort by: accession, proteinName, gene"New value: +"Sort field: accession, proteinName, or gene"
    • removedInput schema / properties / sort_field / title
      Removed value: -"Sort Field"
  2. First observed

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 full burden. It describes the return format as a dict but does not disclose potential side effects, error conditions, or read-only nature. It is adequate but lacks detail on behavior beyond the return.

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: two sentences and a return type line. Every sentence is valuable and front-loaded with the main purpose. No wasted words.

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 5 parameters, an output schema, and no annotations, the description is mostly complete: it explains the main purpose and return format. It does not explain how optional parameters like keyword or sorting work, but these are covered by schema. Slightly lacking in contextual depth.

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 baseline is 3. The description adds no additional meaning beyond the schema descriptions; it does not elaborate on how parameters interact or provide examples.

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 identifies the tool as searching for proteins within a specific PRIDE mass spectrometry project. It uses specific verbs ('Search for') and resources ('proteins identified in a specific PRIDE mass spectrometry project'), and it is well-distinguished from sibling tools like bc_search_pride_projects and bc_get_pride_project.

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

Usage Guidelines4/5

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

The description states the tool is 'useful for finding specific proteins in proteomics datasets,' which implies when to use it. However, it does not explicitly mention when not to use it or provide alternatives among siblings, lacking full exclusions.

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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