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yeyuan98

BioMCP

by yeyuan98
OverviewSchemaSourceRelated ServersDiscussionsAdmin
TypeScript
Remote

article_get

Read-only

Retrieve biomedical articles by PMID, PMCID, or DOI, including preprint versions and funders. Access forward/backward citations from Europe PMC, Semantic Scholar, and OpenCitations.

Instructions

Get article by PMID/PMCID/DOI. Preprint DOIs (bioRxiv/medRxiv, e.g. "10.1101/2025.03.05.641768" or new prefix "10.64898/...") return the preprint record: all versions, license, category, funders, JATS full-text URL, published-version mapping, and (with sections=["citation"]) Europe PMC preprint citations. Journal-article citation: fast mode (~4s, 4 providers, auto-fallback to PubMed) or full mode (~15-30s, all 5 providers incl. PubMed). Forward citation lists come from Europe PMC, Semantic Scholar, and OpenCitations; Crossref provides counts and references only.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesArticle identifier: PMID (numeric, e.g. "12345"), PMCID (e.g. "PMC1234567"), DOI (e.g. "10.1038/s41586-021-03819-2"), or preprint DOI (e.g. "10.1101/2021.10.25.465764", "10.64898/2026.08.11.744243")
limitNoMaximum items per section (e.g., 20 citations)
sectionsNoSections to include. Use ["citation"] for citation data, ["all"] for everything.
citation_modeNoFast: Europe PMC, Semantic Scholar, OpenCitations, Crossref counts/references (~4s). Full: All 5 providers incl. PubMed (~15-30s). Fast mode auto-falls back to PubMed when other providers return no items.fast
citation_directionNoCitation direction: "forward" (articles citing this one), "backward" (references), "both" (default)both

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.5.0
    • changedInput schema / properties / id / description
      Previous value: -"Article identifier: PMID (numeric, e.g. \"12345\"), PMCID (e.g. \"PMC1234567\"), or DOI (e.g. \"10.1038/s41586-021-03819-2\")"New value: +"Article identifier: PMID (numeric, e.g. \"12345\"), PMCID (e.g. \"PMC1234567\"), DOI (e.g. \"10.1038/s41586-021-03819-2\"), or preprint DOI (e.g. \"10.1101/2021.10.25.465764\", \"10.64898/2026.08.11.744243\")"
  2. Changed1 schema field changedv0.7.1
    • changedInput schema / properties / citation_mode / description
      Previous value: -"Fast: Europe PMC, Semantic Scholar, Crossref (~4s). Full: All 5 providers (~15-30s). Fast mode auto-falls back to PubMed when other providers return no items."New value: +"Fast: Europe PMC, Semantic Scholar, OpenCitations, Crossref counts/references (~4s). Full: All 5 providers incl. PubMed (~15-30s). Fast mode auto-falls back to PubMed when other providers return no items."
  3. First observedv0.1.8

TDQS

A4.2/5.0
Behavior5/5

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

Beyond the readOnlyHint annotation, the description discloses substantial behavioral detail: preprint records return specific fields, citation modes have different providers and latencies, fast mode auto-falls back to PubMed, and Crossref's role is limited to counts/references. This gives the agent a rich, accurate mental model of the tool's behavior.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is dense but well-structured, front-loading the core purpose and then expanding into preprint and citation specifics. Some sentences are long and packed with details, but every clause contributes useful information, making it appropriately sized for the tool's complexity.

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?

The description thoroughly covers preprint handling and citation behavior, but it leaves several section enum values (core, oa, annotations, graph) undefined, and with no output schema, it does not explain the default return structure for a basic request. This leaves some ambiguity for agents needing to choose sections or interpret results.

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 baseline is 3. The description enriches citation_mode with provider timing and the preprint DOI behavior with record contents, but it does not add meaningfully to parameters like limit or sections beyond what the schema already states.

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 opens with 'Get article by PMID/PMCID/DOI', a specific verb and resource that clearly defines a lookup tool. It distinguishes itself from article_search by focusing on identifier-based retrieval, and the detailed preprint/citation behavior further clarifies its scope.

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 clearly implies use when you have an article identifier, and it provides concrete guidance on choosing citation modes (fast vs. full) and sections. However, it does not explicitly state when to prefer this tool over alternatives like article_search, leaving that distinction implicit.

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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