Skip to main content
Glama
SuyashEkhande

PubMed Advanced MCP Server

link_to_databases

Retrieve linked biological records from NCBI databases for a PubMed article, including genes, proteins, structures, clinical variants, SNPs, pathways, and compounds.

Instructions

Find records in other NCBI databases linked to an article.

Maps from literature to biological knowledge bases.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidYesSource PubMed ID
target_databasesYesDatabases to link to: - "gene": Associated genes - "protein": Related proteins - "structure": 3D molecular structures - "clinvar": Clinical variants - "snp": Genetic variants - "biosystems": Biological pathways - "pccompound": Chemical compounds

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior2/5

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

With no annotations provided, the description carries full responsibility for behavioral disclosure. It only states what the tool does (finds linked records) without describing any constraints, side effects, return characteristics, or potential limitations such as pagination or database availability. This is a significant gap for a tool that accesses external databases, as the agent cannot anticipate whether the operation is read-only or if any parameters are ignored.

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 extremely concise, consisting of two short sentences that immediately communicate the core function. Every word adds value, with no redundancy or filler. This is an example of efficient, front-loaded writing.

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

Completeness3/5

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

Given the tool's simplicity and the fact that an output schema exists (so return values need not be explained), the description is minimally adequate. However, it lacks usage guidance and behavioral transparency, which prevents it from being fully complete. For a simple look-up tool, this is sufficient but not exemplary.

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?

The input schema provides 100% description coverage for both parameters, with clear explanations for 'pmid' and the list of possible 'target_databases' values. The description itself adds no additional semantic detail beyond the schema, but the schema is self-sufficient, so a 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 the tool's function: 'Find records in other NCBI databases linked to an article.' This specifies a verb and resource, and the second sentence 'Maps from literature to biological knowledge bases' further clarifies the purpose. It distinguishes from sibling tools focused on fetching articles or searching, as this unique cross-linking capability is not offered elsewhere.

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 context ('Maps from literature to biological knowledge bases') but does not explicitly state when to use this tool versus alternatives, nor does it provide exclusions. There is no mention of when not to use it or what other tools might be better suited, leaving the agent to infer the appropriate scenario from the sibling names.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/SuyashEkhande/Pubmed-MCP-Advanced'

If you have feedback or need assistance with the MCP directory API, please join our Discord server