Skip to main content
Glama

Noodle Biomedical Literature Discovery MCP

by io.github.helena-bioinformatics

Get publication details by PMID

get_publication_details
Read-onlyIdempotent

Retrieve one complete public bibliographic record by PMID after search. Results are for literature discovery and professional review, not diagnosis or treatment.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pmidYesOne PubMed identifier to look up in Noodle's current public corpus, as 1 to 12 digits without a PMID prefix.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
publicationYes
usage_boundaryYes
contract_versionYes

TDQS

A4.1/5.0
Behavior3/5

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

Annotations already cover read-only, idempotent, non-destructive behavior. The description adds useful context about returning a complete public bibliographic record and the intended literature-discovery purpose, but it does not disclose additional behavioral details beyond those annotations.

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?

Two concise sentences front-load the core action and scope, with the usage caveat kept brief. Every sentence contributes meaningful information without redundancy.

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?

For a single-parameter, read-only lookup with a full input schema and an output schema present, the description covers what the tool does, when to use it, and its appropriate context. No critical information is missing for correct invocation.

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 fully documents the only parameter, pmid, including format and meaning. The description adds no significant parameter-level detail, so baseline 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 states a specific verb ('Retrieve'), a specific resource ('one complete public bibliographic record'), and the exact identifier type ('by PMID'). This clearly separates it from sibling search or neighborhood tools, which have different scopes.

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 phrase 'after search' gives clear context that this tool is used to retrieve details for a PMID already identified via search. It does not explicitly name alternatives or state when not to use it, but the intended usage is reasonably clear.

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

All Noodle Biomedical Literature Discovery MCP toolsInspect
Try in Browser
RayrunBuild, deploy, and operate MCP servers without becoming an infrastructure team.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

TDQS

A3.9/5.0
Disambiguation4/5

The search and corpus tools are clearly distinct, and the two detail and two neighborhood tools are parallel but differentiated by identifier type (PMID vs. Noodle work ID). The main ambiguity is that get_publication_details and get_work_details both retrieve full records, so agents must understand which identifier they have. support_helena is unrelated but unambiguously separated.

Naming Consistency4/5

Most tools follow a consistent snake_case get_<resource>_<scope> pattern, and search_biomedical_literature fits the retrieval theme. support_helena is a minor outlier because it uses a different action verb and target, but it does not break the overall naming style.

Tool Count5/5

Seven tools is well-scoped for a read-only literature discovery server: corpus summary, semantic search, two lookup modes, two neighborhood exploration modes, and one support action. The count feels intentional and each tool serves a distinct part of the discovery workflow.

Completeness4/5

The read-only discovery surface is largely complete with corpus metadata, search, detailed record retrieval, and neighborhood exploration. A minor gap is that direct retrieval is only by PMID or Noodle work ID, not by DOI/PMCID, though search can serve as a workaround.

Resources