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. Abstracts are included by default; include_abstract: false omits them from every result for a response about a third the size, and biorxiv_get_preprint returns the abstract for up to 10 DOIs per call. 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. A token EuropePMC does not recognize fails with invalid_cursor_mark.
`include_abstract`	No	Include each result's abstract. Defaults to true. false omits the abstract from every result, enriched and EuropePMC-fallback alike, and keeps every other field.

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`notice`	No	Present when zero results are returned: on a cursor_mark page past the last match, says the list is exhausted; otherwise echoes the query and suggests how to broaden it. Also present when abstracts for results shown with EuropePMC metadata only could not be retrieved, which leaves those results without one.
`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.

Changed5 schema fields changedSep 23, 2026

addedInput schema / properties / include_abstract

Added value: +{
+  "default": true,
+  "description": "Include each result's abstract. Defaults to true. false omits the abstract from every result, enriched and EuropePMC-fallback alike, and keeps every other field.",
+  "type": "boolean"
+}

changedOutput schema / properties / notice / description

Previous value: -"Present when zero results are returned. On a cursor_mark page past the last match, says the list is exhausted; otherwise echoes the query and suggests how to broaden it."New value: +"Present when zero results are returned: on a cursor_mark page past the last match, says the list is exhausted; otherwise echoes the query and suggests how to broaden it. Also present when abstracts for results shown with EuropePMC metadata only could not be retrieved, which leaves those results without one."

changedOutput schema / properties / preprints / items / properties / abstract / description

Previous value: -"Abstract text."New value: +"Abstract text. Omitted when include_abstract is false. On a EuropePMC-fallback record, absent when EuropePMC holds none or the abstract lookup failed — the notice says when it failed."

addedOutput schema / properties / preprints / items / properties / awards

Added value: +{
+  "description": "Grant award numbers from the funding statement, verbatim and deduplicated — one value can hold several grants run together without a separator. Absent when none, and on EuropePMC-only fallback records. Funder names are not included: api.biorxiv.org attributes them to unrelated organizations.",
+  "items": {
+    "description": "One award value as upstream records it.",
+    "type": "string"
+  },
+  "type": "array"
+}

removedOutput schema / properties / preprints / items / properties / funder

Removed value: -{
-  "description": "Funder information.",
-  "type": "string"
-}

Changed4 schema fields changedSep 23, 2026

changedInput schema / properties / cursor_mark / description

Previous value: -"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."New value: +"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. A token EuropePMC does not recognize fails with invalid_cursor_mark."

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_date_range`: date_from or date_to is malformed, or date_from is after date_to. `search_unavailable`: EuropePMC search endpoint is unreachable or returns a server error. `rate_limited`: The EuropePMC search endpoint rejected the keyword search with HTTP 429. Distinct from a rate-limited enrichment call, which degrades to EuropePMC-only metadata instead of failing. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_date_range`: date_from or date_to is malformed, or date_from is after date_to. `search_unavailable`: EuropePMC search endpoint is unreachable, returns a server error, or answers a first-page search without a result list on every retry. `invalid_cursor_mark`: EuropePMC answers a cursor_mark page request without a result list on every retry — the token is malformed or not one EuropePMC issued. `rate_limited`: The EuropePMC search endpoint rejected the keyword search with HTTP 429. Distinct from a rate-limited enrichment call, which degrades to EuropePMC-only metadata instead of failing. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "invalid_date_range",
-  "search_unavailable",
-  "rate_limited"
-]New value: +[
+  "invalid_date_range",
+  "search_unavailable",
+  "invalid_cursor_mark",
+  "rate_limited"
+]

changedOutput schema / properties / notice / description

Previous value: -"Recovery hint when zero results are returned — echoes query and suggests how to broaden."New value: +"Present when zero results are returned. On a cursor_mark page past the last match, says the list is exhausted; otherwise echoes the query and suggests how to broaden it."

First observedSep 19, 2026

TDQS

A4.9/5.0

Behavior5/5

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

The description adds substantial behavioral context beyond the readOnlyHint and openWorldHint annotations, including EuropePMC indexing lag, rate-limit failure semantics with a retryable rate_limited error, and how rate-limited enrichment differs by marking records with enrichment_error. It also explains default server coverage and abstract-size tradeoffs. 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?

The description is dense but every sentence earns its place: purpose, query composition, server scope, recency caveat, abstract tradeoff, and error semantics. It is front-loaded with the core action and spends no words on filler.

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 an 8-parameter tool with an output schema, the description covers selection criteria, paging context, server defaults, latency caveats, error handling, and sibling alternatives. The schema covers parameter formatting, so nothing critical is left unexplained.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The input schema already covers all parameters with descriptions, giving a baseline of 3. The tool description adds meaningful semantics by explaining how author maps to an AUTH: field query and is ANDed with the keyword query, and how include_abstract affects response size and the resulting enrichment behavior.

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 a specific verb and resource: searching preprints by keyword and/or author, then enriching DOIs with full metadata. It also distinguishes itself from biorxiv_list_recent, so an agent can tell it apart from a sibling without inspecting schemas.

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 guidance on when to use this tool vs. biorxiv_list_recent (for preprints posted within the last day), and explains the alternative path of biorxiv_get_preprint for retrieving abstracts after omitting them. It also specifies that query, author, or both are valid inputs.

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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