biorxiv-mcp-server

Get Published Journal Version

biorxiv_get_published_version

Read-onlyIdempotent

Resolve a DOI to its preprint-to-journal crosswalk record — preprint DOI, journal DOI, journal name, published date, and corresponding author details — from either side: a preprint DOI (10.1101/ or 10.64898/) finds the journal article it was published as, and any other DOI is read as a journal article's and finds the bioRxiv or medRxiv preprint it was posted as. Use when biorxiv_get_preprint shows a publishedJournalDoi and you need the journal details, or when you hold a journal article and want its preprint. bioRxiv and medRxiv share their DOI prefixes, so server="both" (the default) checks both in parallel and the response reports which server answered. 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 when no server holds the preprint, it lists no journal version, or no preprint is recorded for the journal DOI.

Input Schema

Name	Required	Description	Default
`doi`	Yes	DOI to resolve: a preprint DOI (e.g. 10.1101/2024.01.15.575123 or 10.64898/2026.05.07.723463) or a journal article DOI (e.g. 10.1016/j.cell.2020.01.001). A doi.org or biorxiv.org/medrxiv.org article URL or a doi: prefix is accepted and stripped to the bare DOI, as is a vN, .full, or .pdf suffix; a journal DOI keeps its own components (10.7554/eLife.55185.sa1 is not 10.7554/eLife.55185). Cold Spring Harbor Laboratory Press journal DOIs (10.1101/gr.…, 10.1101/gad.…, 10.1101/lm.…) share the preprint prefix and cannot be resolved by 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

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, in bare form: the input itself when it was a preprint DOI, or the preprint the crosswalk links to the input when it was a journal DOI.
`preprintDate`	No	Preprint posting date (YYYY-MM-DD) from the crosswalk record, or from the preprint's first revision when the crosswalk has none — the first posting for most preprints. medRxiv records some 10.64898/ preprints twice with different posting dates; this is the first record listed.
`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.

Changed3 schema fields changedOct 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). 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."New value: +"DOI to resolve: a preprint DOI (e.g. 10.1101/2024.01.15.575123 or 10.64898/2026.05.07.723463) or a journal article DOI (e.g. 10.1016/j.cell.2020.01.001). A doi.org or biorxiv.org/medrxiv.org article URL or a doi: prefix is accepted and stripped to the bare DOI, as is a vN, .full, or .pdf suffix; a journal DOI keeps its own components (10.7554/eLife.55185.sa1 is not 10.7554/eLife.55185). Cold Spring Harbor Laboratory Press journal DOIs (10.1101/gr.…, 10.1101/gad.…, 10.1101/lm.…) share the preprint prefix and cannot be resolved by DOI."

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

Previous 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."New value: +"Machine-readable failure mode. Declared by this tool: `doi_not_found`: No attempted server holds the preprint, neither the crosswalk nor its preprint record lists a journal version, or the crosswalk links no preprint to the journal DOI given. `invalid_doi_format`: The input does not match the 10.NNNN/ DOI 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."

changedOutput schema / properties / preprintDoi / description

Previous value: -"The preprint DOI that was resolved, in bare form."New value: +"The preprint DOI, in bare form: the input itself when it was a preprint DOI, or the preprint the crosswalk links to the input when it was a journal DOI."

Changed1 schema field changedOct 18, 2026

changedOutput schema / properties / preprintDate / description

Previous value: -"Date the preprint was first posted."New value: +"Preprint posting date (YYYY-MM-DD) from the crosswalk record, or from the preprint's first revision when the crosswalk has none — the first posting for most preprints. medRxiv records some 10.64898/ preprints twice with different posting dates; this is the first record listed."

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 only cover readOnly/openWorld/idempotent, but the description adds real operational context: server="both" queries both servers in parallel and the response reports which one answered, the degraded case where a journal DOI returns without journal name or date plus an explanatory notice, and the exact not-found conditions. It also flags a genuine edge case (CSHL Press 10.1101/gr., gad., lm. DOIs sharing the preprint prefix).

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?

A single dense block, but front-loaded with the action and return shape before moving to usage, server behavior, and error semantics. Almost every clause carries information; the field enumeration is slightly redundant given an output schema exists.

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 a two-parameter read tool with full schema coverage and an output schema, nothing an agent needs is missing: direction rules, default server behavior, partial-result semantics, and failure modes are all stated. The field list is a bonus rather than a necessity.

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 coverage is 100%, so the baseline is 3; the description goes beyond it by explaining the direction semantics tied to DOI prefix (10.1101/ and 10.64898/ mean preprint, anything else means journal) and by explaining why the default server="both" exists and what the response reports. It doesn't restate the normalization rules, but the schema already owns those.

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 and resource — 'Resolve a DOI to its preprint-to-journal crosswalk record' — and enumerates the returned fields (preprint DOI, journal DOI, journal name, published date, author details). It also clarifies the bidirectional resolution (preprint DOI → journal article, any other DOI → preprint), which makes it unmistakable versus the sibling list/search tools.

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?

Names an explicit trigger and its alternative: 'Use when biorxiv_get_preprint shows a `publishedJournalDoi` and you need the journal details, or when you hold a journal article and want its preprint.' That is a concrete when-to-use routed through a named sibling rather than an inference.

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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