biorxiv-mcp-server

Get Published Journal Version

biorxiv_get_published_version

Read-onlyIdempotent

Resolve a preprint DOI to its full journal publication record — journal DOI, journal name, published date, and corresponding author details. Use when the preprint's publishedJournalDoi field from biorxiv_get_preprint is present and you need the full crosswalk metadata. bioRxiv and medRxiv share their DOI prefixes, so server="both" (the default) checks both in parallel and the response reports which server answered. Works for 10.1101/ and 10.64898/ DOIs alike; when the crosswalk holds no record for a published preprint, the journal DOI still comes back from the preprint's own record, without journal name or date, and a notice says so. Returns a not-found error only when no server holds the preprint or it lists no journal version at all.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`doi`	Yes	Preprint DOI to resolve (e.g. 10.1101/2024.01.15.575123 or 10.64898/2026.05.07.723463). A doi.org or biorxiv.org/medrxiv.org article URL, a doi: prefix, or a vN / .full suffix is accepted and stripped to the bare DOI.
`server`	No	Server the preprint was posted on. "both" (default) checks bioRxiv and medRxiv in parallel — use it when the DOI alone does not tell you which server holds the preprint.	both

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`notice`	No	Present when publishedDoi came from the preprint's own record because the crosswalk had none: says why publishedJournal and publishedDate are absent.
`server`	No	The server that returned this published record — never "both".
`preprintDoi`	No	The preprint DOI that was resolved, in bare form.
`preprintDate`	No	Date the preprint was first posted.
`publishedDoi`	No	The journal publication DOI.
`preprintTitle`	No	Title of the preprint.
`publishedDate`	No	Journal publication date (YYYY-MM-DD). Absent when the crosswalk holds no record for this preprint — see notice.
`preprintAuthors`	No	Preprint author list.
`preprintAbstract`	No	Preprint abstract.
`preprintCategory`	No	Subject category.
`publishedJournal`	No	Name of the publishing journal. Absent when the crosswalk holds no record for this preprint — see notice.
`preprintAuthorCorresponding`	No	Corresponding author name.
`preprintAuthorCorrespondingInstitution`	No	Corresponding author institution.

Schema Changelog

Changes observed during successful MCP inspections.

Changed6 schema fields changedSep 23, 2026

changedInput schema / properties / doi / description

Previous value: -"Preprint DOI to resolve (e.g. 10.1101/2024.01.15.575123 or 10.64898/2026.05.07.723463)."New value: +"Preprint DOI to resolve (e.g. 10.1101/2024.01.15.575123 or 10.64898/2026.05.07.723463). A doi.org or biorxiv.org/medrxiv.org article URL, a doi: prefix, or a vN / .full suffix is accepted and stripped to the bare DOI."

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `doi_not_found`: Crosswalk endpoint returns an empty collection on every attempted server. `invalid_doi_format`: The input DOI does not match the 10.NNNN/ pattern. `upstream_unavailable`: No attempted server returned a record and at least one lookup failed against api.biorxiv.org. `rate_limited`: No attempted server returned a record and at least one lookup was rejected with HTTP 429 by api.biorxiv.org. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `doi_not_found`: No attempted server holds the preprint, or neither the crosswalk nor its preprint record lists a journal version. `invalid_doi_format`: The input DOI does not match the 10.NNNN/ pattern, even after URL, doi:, and suffix stripping. `upstream_unavailable`: No published record was established and at least one crosswalk or preprint lookup failed against api.biorxiv.org. `rate_limited`: No published record was established and at least one crosswalk or preprint lookup was rejected with HTTP 429 by api.biorxiv.org. Other values are possible when a failure originates below the handler."

addedOutput schema / properties / notice

Added value: +{
+  "description": "Present when publishedDoi came from the preprint's own record because the crosswalk had none: says why publishedJournal and publishedDate are absent.",
+  "type": "string"
+}

changedOutput schema / properties / preprintDoi / description

Previous value: -"The preprint DOI that was resolved."New value: +"The preprint DOI that was resolved, in bare form."

changedOutput schema / properties / publishedDate / description

Previous value: -"Journal publication date (YYYY-MM-DD)."New value: +"Journal publication date (YYYY-MM-DD). Absent when the crosswalk holds no record for this preprint — see notice."

changedOutput schema / properties / publishedJournal / description

Previous value: -"Name of the publishing journal."New value: +"Name of the publishing journal. Absent when the crosswalk holds no record for this preprint — see notice."

First observedSep 19, 2026

TDQS

A4.8/5.0

Behavior5/5

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

Annotations already declare readOnly, idempotent, and open-world hints. The description adds valuable behavioral detail: parallel server checking, DOI prefix compatibility, the fallback behavior when the crosswalk has no record, and the precise error condition. This goes well beyond what annotations provide.

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 front-loaded with purpose, then usage, then edge cases. Every sentence contributes new information without redundancy. It's longer than minimal but efficient for the complexity covered.

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?

An output schema exists, so return values needn't be detailed. The description covers all operational aspects: what it resolves, when to use it, how server selection works, edge cases, and error conditions. Complete 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.

Parameters5/5

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

Schema already documents both parameters with examples. The description adds normalization rules for the DOI (accepting URLs, doi: prefix, vN/.full suffixes) and explains the 'both' server behavior (parallel check and response reporting). This is meaningful added value beyond the schema.

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?

States a specific verb 'Resolve', a specific resource 'preprint DOI', and the output fields (journal DOI, journal name, published date, corresponding author details). Clearly distinguishes from siblings like biorxiv_get_preprint by focusing on the published journal version rather than the preprint itself.

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?

Provides an explicit trigger condition: use when the preprint's `publishedJournalDoi` field is present and you need the full crosswalk metadata. Does not explicitly name alternative tools or state when-not-to-use, but the condition is specific enough to guide selection. Could be improved by naming a sibling for the opposite case.

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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