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

Name	Required	Description	Default
`limit`	No	Maximum results to return. Defaults to 25. Up to 100 per call: a larger value returns the first 100 and says so, and nextCursorMark continues the ranked list.
`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 the search and its enrichment: "biorxiv" or "medrxiv" returns only that server's preprints; "both" searches both and checks each matching DOI 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

Name	Required	Description
`cap`	No	Results one call returns at most (100). Set with truncated.
`error`	No	Present when the call failed. Absent on success.
`shown`	No	Results on this page. Set with truncated.
`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 limit was above the 100-result cap per call, and 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.
`truncated`	No	True when limit asked for more than the 100 results one call returns and this page holds all 100 — continue with nextCursorMark.
`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.

Changed1 schema field changedOct 28, 2026

changedInput schema / properties / server / description

Previous value: -"Server scope for enrichment. \"both\" checks all matching DOIs on both servers."New value: +"Server scope for the search and its enrichment: \"biorxiv\" or \"medrxiv\" returns only that server's preprints; \"both\" searches both and checks each matching DOI on both servers."

Changed3 schema fields changedOct 23, 2026

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 not a real calendar date (2024-02-30, 2024-13-01), 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."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_date_range`: date_from or date_to is not a real calendar date (2024-02-30, 2024-13-01), or date_from is after date_to. `search_unavailable`: EuropePMC search endpoint is unreachable, returns a server error, or answers without a result list on every retry. On a cursor_mark page, HTTP 503 or a missing result list on every retry is this reason only when the first page of the same query fails too, or no time is left to check it. `invalid_cursor_mark`: EuropePMC answers a cursor_mark page with HTTP 503 or without a result list on every retry while the first page of the same query answers — 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 / preprints / items / properties / server / description

Previous value: -"Source server (biorxiv or medrxiv)."New value: +"Server the preprint was found on — accepted as the server input of every tool. Present on enriched records only."

addedOutput schema / properties / preprints / items / properties / server / enum
```
Added value: +[
+  "biorxiv",
+  "medrxiv"
+]
```

Changed7 schema fields changedOct 18, 2026

changedInput schema / properties / limit / description

Previous value: -"Maximum results to return (1–100). Defaults to 25."New value: +"Maximum results to return. Defaults to 25. Up to 100 per call: a larger value returns the first 100 and says so, and nextCursorMark continues the ranked list."

changedInput schema / properties / limit / maximum
```
Previous value: -100New value: +1000
```

addedOutput schema / properties / cap

Added value: +{
+  "description": "Results one call returns at most (100). Set with truncated.",
+  "type": "number"
+}

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. Also present when abstracts for results shown with EuropePMC metadata only could not be retrieved, which leaves those results without one."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 limit was above the 100-result cap per call, and when abstracts for results shown with EuropePMC metadata only could not be retrieved, which leaves those results without one."

changedOutput schema / properties / queryEcho / properties / limit / description

Previous value: -"Maximum results requested."New value: +"Maximum results requested from EuropePMC: the limit input, capped at 100 per call."

addedOutput schema / properties / shown

Added value: +{
+  "description": "Results on this page. Set with truncated.",
+  "type": "number"
+}

addedOutput schema / properties / truncated

Added value: +{
+  "description": "True when limit asked for more than the 100 results one call returns and this page holds all 100 — continue with nextCursorMark.",
+  "type": "boolean"
+}

Changed3 schema fields changedOct 15, 2026

addedInput schema / properties / date_from / pattern
```
Added value: +"^\\d{4}-\\d{2}-\\d{2}$"
```
addedInput schema / properties / date_to / pattern
```
Added value: +"^\\d{4}-\\d{2}-\\d{2}$"
```

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, 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."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_date_range`: date_from or date_to is not a real calendar date (2024-02-30, 2024-13-01), 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."

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

A4.4/5.0

Behavior3/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety profile is covered and the description's remaining job is failure and cost behavior, which it does well: HTTP 429 becomes a retryable rate_limited error with a wait in seconds, while an enrichment-side 429 degrades gracefully to enrichment_error: "rate_limited" on the record. It also discloses the 1–2 day EuropePMC indexing lag. It stops short of describing result ordering or what the enrichment fields look like, so it sits at a solid but not exceptional 3 given the annotation floor.

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?

Front-loaded with purpose and the query/author contract, then layered cost, latency, and error behavior — a sensible ordering with almost no filler. A few clauses restate schema content (abstract omission, server default), costing a point on strict economy for an otherwise dense paragraph.

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, open-world search tool with an output schema, the description covers everything an agent needs before calling: input contract, pagination via cursor_mark, indexing recency limits, two distinct 429 failure modes, and a response-size lever. Return-value shape is correctly delegated to the output schema.

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?

Schema description coverage is 100%, so the baseline is 3; the description earns an extra point by adding semantics the schema does not carry, notably that author is mapped to an EuropePMC AUTH: field query ANDed with the keyword query, that omitting abstracts yields roughly a third the response size, and that include_abstract applies uniformly to enriched and fallback records. The duplicated limit/server explanations overlap with the schema rather than extending it.

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?

Names a specific verb and resource ("search preprints by keyword and/or author") and explains the two-stage retrieval model: EuropePMC relevance ranking plus bioRxiv/medRxiv metadata enrichment on matching DOIs. It explicitly separates itself from the sibling biorxiv_list_recent and points to biorxiv_get_preprint, so an agent can route correctly without opening any schema.

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?

States the input combinations that trigger the tool (keyword, author, or both), gives the exact exclusion condition ("for preprints posted within the last day, prefer biorxiv_list_recent"), and names biorxiv_get_preprint as the alternate path for abstracts. Both when-to-use and when-not-to-use are present with named alternatives.

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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Search Preprints by Keyword

Input Schema

Output Schema

Schema Changelog

TDQS

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