biorxiv-mcp-server

Search Preprints by Keyword

biorxiv_search_preprints

Read-only

Search preprints by keyword and/or author using EuropePMC for relevance ranking, then enrich matching DOIs with full bioRxiv/medRxiv metadata. Provide a keyword query, an author name, or both — author maps to an EuropePMC AUTH: field query and is ANDed with the keyword query. Covers both servers by default. EuropePMC indexes new preprints within 1–2 days of posting; for preprints posted within the last day, prefer biorxiv_list_recent. A EuropePMC rate limit (HTTP 429) fails the call with a retryable rate_limited error carrying the wait in seconds — a rate-limited metadata enrichment does not, and instead marks the affected record enrichment_error: "rate_limited".

Input Schema

TableJSON Schema

Name	Required	Description	Default
`limit`	No	Maximum results to return (1–100). Defaults to 25.
`query`	No	Keyword search query. Optional when author is provided — supply at least one of query or author.
`author`	No	Author name to filter by, mapped to an EuropePMC AUTH:"…" field query and ANDed with the keyword query. Optional when query is provided (e.g. "Jennifer Doudna").
`server`	No	Server scope for enrichment. "both" checks all matching DOIs on both servers.	both
`date_to`	No	Latest first-publication date filter (YYYY-MM-DD).
`date_from`	No	Earliest first-publication date filter (YYYY-MM-DD).
`cursor_mark`	No	Opaque page token for ranked EuropePMC results. Omit for the first page; pass the nextCursorMark returned by a prior call to fetch the next page. Pages through the same ranked list rather than raising limit.

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`notice`	No	Recovery hint when zero results are returned — echoes query and suggests how to broaden.
`preprints`	No	Search results, ranked by EuropePMC relevance.
`queryEcho`	No	Echo of the parameters used to produce this result set — lets callers verify what was sent.
`totalCount`	No	Total preprints matching the query in EuropePMC (hitCount) — the true upstream grand total, not the number of results returned.
`nextCursorMark`	No	Opaque token for the next page of ranked results. Present only when more results exist beyond this page; pass it back as cursor_mark. Absent on the last page.
`partial_results`	No	True when one or more DOIs failed bioRxiv enrichment and fell back to EuropePMC metadata.

Schema Changelog

Changes observed during successful MCP inspections.

First observedSep 19, 2026

TDQS

A4.7/5.0

Behavior5/5

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

Annotations already signal read-only and open-world behavior, but the description adds substantial value: EuropePMC indexing delay of 1–2 days, rate-limit failure semantics with retryable errors, and enrichment failure handling via enrichment_error: "rate_limited". No contradiction with annotations exists.

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?

Every sentence earns its place: core behavior, parameter combination rule, recency caveat with alternative, and error behavior. The most important functional information is front-loaded, and the content is dense without fluff.

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?

The description is complete for a search tool with a rich output schema and annotations. It covers behavior, default scope, timing caveats, error handling, and the key alternative, leaving nothing necessary for an agent to call it correctly.

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 does not meaningfully add beyond the schema: the AUTH mapping and ANDing of author is already in the author parameter description, and the server default is already in the server parameter description. The description reinforces usage constraints but does not introduce new parameter semantics.

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 preprints by keyword and/or author, with EuropePMC relevance ranking and bioRxiv/medRxiv metadata enrichment. It is clearly differentiated from siblings like biorxiv_get_preprint and biorxiv_get_fulltext by framing this as a search/enumerate operation, and it even names biorxiv_list_recent as the alternative for very recent preprints.

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 gives explicit usage context: supply a keyword, an author, or both; author is ANDed with the keyword. It also gives a concrete when-not-to-use rule by directing users to biorxiv_list_recent for preprints posted within the last day, and it notes the default server coverage.

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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