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yeyuan98

BioMCP

by yeyuan98
OverviewSchemaSourceRelated ServersDiscussionsAdmin
TypeScript
Remote

article_search

Read-only

Search biomedical literature across multiple sources with one query; federated search and deduplication deliver relevant articles from PubMed, EuropePMC, arXiv, and more.

Instructions

Search literature across multiple backends with federated search and deduplication

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMaximum results to return. Applied to final deduplicated results, not per-source. Each source may fetch more internally before deduplication.
queryYesSearch query (title, abstract, or keyword). Journal scoping: PubMed matches full journal names and NLM abbreviations; EuropePMC JOURNAL:"..." filters require the NLM abbreviation (e.g. "N Engl J Med")
offsetNoResult offset. EuropePMC and preprint_only windows are capped at 1000 rows; use narrower queries or another source for deeper results
sourceNoSpecific source to search. "preprint_only" searches ONLY bioRxiv+medRxiv preprints (bioRxiv/medRxiv DOIs, abstracts, citation counts, via Europe PMC's preprint index); "arxiv" searches the arXiv preprint server (quotes, parentheses, and field prefixes like ti:/au: are stripped from the query for arXiv only). Default (unset) = federated journal-literature search across PubMed, EuropePMC, Semantic Scholar, arXiv, PubTator, LitSense; bioRxiv/medRxiv preprints are NOT included unless explicitly requested via preprint_only.
dateRangeNoDate range as YYYY-MM-DD/YYYY-MM-DD. Open-ended: "2020-01-01/" or "/2023-12-31". Only pubmed, europepmc, semantic_scholar, preprint_only, and arxiv support this.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed4 schema fields changedv1.5.0
    • changedInput schema / properties / dateRange / description
      Previous value: -"Date range as YYYY-MM-DD/YYYY-MM-DD. Open-ended: \"2020-01-01/\" or \"/2023-12-31\". Only pubmed, europepmc, semantic_scholar support this."New value: +"Date range as YYYY-MM-DD/YYYY-MM-DD. Open-ended: \"2020-01-01/\" or \"/2023-12-31\". Only pubmed, europepmc, semantic_scholar, preprint_only, and arxiv support this."
    • changedInput schema / properties / offset / description
      Previous value: -"Result offset. EuropePMC windows are capped at 1000 rows; use narrower queries or another source for deeper results"New value: +"Result offset. EuropePMC and preprint_only windows are capped at 1000 rows; use narrower queries or another source for deeper results"
    • changedInput schema / properties / source / description
      Previous value: -"Specific source to search"New value: +"Specific source to search. \"preprint_only\" searches ONLY bioRxiv+medRxiv preprints (bioRxiv/medRxiv DOIs, abstracts, citation counts, via Europe PMC's preprint index); \"arxiv\" searches the arXiv preprint server (quotes, parentheses, and field prefixes like ti:/au: are stripped from the query for arXiv only). Default (unset) = federated journal-literature search across PubMed, EuropePMC, Semantic Scholar, arXiv, PubTator, LitSense; bioRxiv/medRxiv preprints are NOT included unless explicitly requested via preprint_only."
    • changedInput schema / properties / source / enum
      Previous value: -[
-  "pubmed",
-  "europepmc",
-  "semantic_scholar",
-  "pubtator",
-  "litsense"
-]New value: +[
+  "pubmed",
+  "europepmc",
+  "semantic_scholar",
+  "pubtator",
+  "litsense",
+  "preprint_only",
+  "arxiv"
+]
  2. Changed2 schema fields changedv1.4.2
    • changedInput schema / properties / offset / description
      Previous value: -"Result offset"New value: +"Result offset. EuropePMC windows are capped at 1000 rows; use narrower queries or another source for deeper results"
    • changedInput schema / properties / query / description
      Previous value: -"Search query (title, abstract, or keyword)"New value: +"Search query (title, abstract, or keyword). Journal scoping: PubMed matches full journal names and NLM abbreviations; EuropePMC JOURNAL:\"...\" filters require the NLM abbreviation (e.g. \"N Engl J Med\")"
  3. First observedv0.1.8

TDQS

A3.8/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so safety and open-world behavior are covered. The description adds value by disclosing federated search (multiple backends) and deduplication, which are not in the annotations. It does not mention rate limits or response format, but the schema fills some of that gap.

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 a single sentence that front-loads the core action and key behaviors. It has zero filler and every word contributes meaning, making it appropriately concise and well-structured.

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?

The tool has five well-documented parameters and informative annotations; the description adequately complements the rich schema without redundancy. It doesn't explicitly state the return format, but the tool name and purpose make that largely obvious, and no output schema is present to demand it.

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% with detailed descriptions for all five parameters, so the description need not repeat them. The description adds no parameter-specific semantics beyond the schema; a baseline 3 is appropriate when the schema shoulders the load.

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 and resource: 'Search literature' with 'federated search and deduplication' as distinguishing features. It clearly differentiates from article_get (retrieval) and other entity-specific search tools in the sibling list. The description is informative and not a tautology.

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

Usage Guidelines2/5

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

The description says what the tool does but provides no guidance on when to use it versus alternatives like article_get, nor when not to use it. No exclusions or alternative tools are mentioned. While the schema's source parameter hints at usage scenarios, the description itself lacks this guidance.

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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