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kmaneesh

BioPython MCP Server

by kmaneesh

variant_literature_link

Identify PubMed articles associated with a genetic variant using ClinVar ID or dbSNP rs number. Returns linked PubMed IDs and article summaries.

Instructions

Find literature (PubMed) articles linked to a specific variant.

Uses Entrez ELink to find cross-database relationships between variant databases and PubMed.

Args: variant_id: Variant ID (ClinVar ID or dbSNP rs number) source_db: Source database - "clinvar" or "snp" (default: "clinvar") max_results: Maximum articles to return (default: 10)

Returns: Dictionary containing: - variant_id: Input variant ID - source_db: Source database used - linked_pmids: List of linked PubMed IDs - articles: List of article summaries - count: Number of articles found

Examples: >>> variant_literature_link("12345", source_db="clinvar") >>> variant_literature_link("80357906", source_db="snp", max_results=5)

Notes: - Not all variants have linked literature - Uses Entrez ELink for database cross-referencing - Rate limited (3 req/sec or 10 req/sec with API key)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
variant_idYes
source_dbNoclinvar
max_resultsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

With no annotations, the description carries full disclosure weight. It discloses the use of Entrez ELink, rate limits, and the fact that not all variants have literature. It does not mention any destructive actions, which is appropriate for a read-only lookup tool.

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 well-structured with clear sections (Description, Args, Returns, Examples, Notes). It uses bullet points for clarity and is concise without unnecessary text. Every section adds value.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The description covers purpose, all parameters, return structure, examples, limitations, and rate limits. Given the presence of an output schema, it appropriately summarizes return fields without over-explaining. The context is complete for the tool's complexity.

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

Parameters5/5

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

Schema coverage is 0%, but the description provides detailed parameter explanations in the Args section, including types, defaults, and examples. It explains variant_id as ClinVar ID or dbSNP rs number, source_db options, and max_results behavior. This fully compensates for the lack of schema description.

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 the tool finds literature linked to a specific variant, specifying the verb (find), resource (PubMed articles), and input (variant). It distinguishes from siblings like pubmed_search or entrez_link which have broader or different purposes.

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 provides parameter details, examples, and notes on limitations and rate limits, but does not explicitly guide when to use this tool versus alternatives like entrez_link or pubmed_search. The context of many sibling tools suggests that explicit guidelines would be beneficial.

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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