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pubmed-mcp-server

by cyanheads

Pubmed Convert Ids

pubmed_convert_ids
Read-only

Convert article identifiers between DOI, PMID, and PMCID for PubMed Central articles. Handles up to 50 IDs of a single type per request.

Instructions

Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Only resolves articles indexed in PubMed Central — for articles not in PMC, use pubmed_search_articles instead.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idsYesArticle identifiers to convert. All IDs must be the same type. DOIs: "10.1093/nar/gks1195", PMIDs: "23193287", PMCIDs: "PMC3531190" (the "PMC" prefix is optional — bare digits like "3531190" are also accepted).
idTypeYesThe type of IDs being submitted. Required so the API can unambiguously resolve them.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
recordsYesConversion results, one per input ID
totalConvertedYesNumber of IDs successfully converted
totalSubmittedYesNumber of IDs submitted
Behavior4/5

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

The description adds constraints beyond annotations (readOnlyHint, openWorldHint) by specifying the PMC-only limitation and batch size. It aligns with readOnlyHint as a safe conversion operation. No contradictions.

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 with no wasted words. It front-loads the purpose and immediately provides key constraints and alternatives.

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 the presence of an output schema, the description adequately covers purpose, constraints, and alternatives. It does not detail errors or rate limits but is sufficient for a simple conversion tool with good annotations.

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 coverage is 100%, so the schema already documents both parameters with examples. The description does not add new parameter details beyond what the schema provides, but it reinforces the single-type constraint and limit, earning a baseline score.

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 converts between article identifiers (DOI, PMID, PMCID). It also distinguishes itself from siblings by specifying it only works for articles indexed in PubMed Central and directs users to pubmed_search_articles for non-PMC articles.

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

Usage Guidelines5/5

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

The description provides explicit usage conditions: accepts up to 50 IDs of a single type per request, and resolves only PMC articles. It also tells when not to use this tool and suggests an alternative (pubmed_search_articles).

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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