biorxiv-mcp-server

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  <h1>@cyanheads/biorxiv-mcp-server</h1>
  <p><b>Search and retrieve bioRxiv and medRxiv preprints — by DOI, date interval, or keyword — via MCP. STDIO or Streamable HTTP.</b>
  <div>6 Tools</div>
  </p>
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## Tools

Six tools for working with bioRxiv and medRxiv preprint data:

| Tool | Description |
|:---|:---|
| `biorxiv_get_preprint` | Fetch full metadata, abstract, revision history, and journal crosswalk for one or more preprints by DOI |
| `biorxiv_list_recent` | List preprints posted or updated within a date interval, with optional server and category filters |
| `biorxiv_search_preprints` | Search preprints by keyword and/or author via EuropePMC for relevance ranking, enriched with bioRxiv/medRxiv metadata |
| `biorxiv_get_published_version` | Resolve a preprint DOI to its journal publication record (journal DOI, name, published date) |
| `biorxiv_get_fulltext` | Retrieve a preprint's full text as best-effort Markdown extracted from its rendered HTML article page |
| `biorxiv_list_categories` | List valid subject category strings for bioRxiv and medRxiv |

### `biorxiv_get_preprint`

Fetch preprint metadata by DOI — all revisions in one call.

- Batch fetch up to 10 DOIs in a single request
- Each DOI returns the full revision history in `collection[]` — one API call per DOI, no enumeration loop
- Includes title, authors, abstract, category, license, JATS XML full-text link (`jatsxml`), and published journal DOI when the preprint has been accepted
- Scope to `biorxiv`, `medrxiv`, or `both`; when `both`, each DOI fans out in parallel and partial failures report per-DOI in `failed[]`
- Each `failed[]` entry carries a `reason` (`not_found`, `invalid_doi_format`, `upstream_unavailable`, `rate_limited`) and a `retryable` flag — a DOI is only reported as not found when every attempted server answered
- A lookup the origin rate-limited (HTTP 429) reports as `rate_limited` rather than folding into `upstream_unavailable`, and carries `retryAfter` — the wait in seconds `api.biorxiv.org` asked for

---

### `biorxiv_list_recent`

Page through preprints in a date interval.

- Server-side category filtering via `?category=…` — pass a value from `biorxiv_list_categories`
- Fixed page size of 30 (API constraint); advance with integer `cursor` (0, 30, 60, …)
- Response includes `total` count per server for calculating remaining pages
- When `server="both"`, each server paginates independently; response surfaces per-server pagination state (`{ biorxiv: { cursor, total }, medrxiv: { cursor, total } }`)
- A server whose cursor is past its last page is marked `exhausted: true` — the API reports `total: 0` for an out-of-range cursor, so that count is an artifact rather than the interval total
- One server not answering under `server="both"` is named in `failed[]` rather than dropped; the other server's page is still returned, and a non-empty `failed[]` marks the result set as partial
- Every attempted server failing raises a retryable `upstream_unavailable` (or `rate_limited`) error instead of returning an empty page — nothing answered, so an empty interval was never established

---

### `biorxiv_search_preprints`

Keyword and/or author search with relevance ranking.

- EuropePMC powers relevance ranking (indexes new preprints within 1–2 days of posting); bioRxiv/medRxiv API provides canonical metadata enrichment
- Optional `author` maps to an EuropePMC `AUTH:"…"` field query, ANDed with the keyword query — supply `query`, `author`, or both
- Covers both servers by default; scope down with `server`
- Optional date range filters (`date_from`, `date_to`)
- Enriched results carry the same latest-revision fields `biorxiv_get_preprint` returns — including `type`, `license`, `funder`, and `authorCorrespondingInstitution`
- Enrichment failures degrade gracefully to EuropePMC-only metadata, surfaced via `partial_results` and a per-record `enrichment_error` (`service_error`, `rate_limited`, or `not_found`)
- A EuropePMC rate limit (HTTP 429) raises a retryable `rate_limited` error carrying the origin's `Retry-After` wait — the search is the primary call and has no metadata to fall back on, unlike the enrichment step

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### `biorxiv_get_published_version`

Resolve a preprint DOI to its journal publication crosswalk.

- Uses the `/pubs/{server}/{doi}` endpoint for richer metadata than the `publishedJournalDoi` field in `biorxiv_get_preprint`
- Returns journal DOI, journal name, published date, and corresponding author institution
- Use when the preprint's `publishedJournalDoi` field is present and you need the full crosswalk record
- Scope to `biorxiv`, `medrxiv`, or `both`; `both` is the default because the two servers share the `10.1101/` DOI prefix, and the output `server` field names the one that answered
- No server answering raises a retryable `upstream_unavailable`, or `rate_limited` with the origin's wait when the failure was an HTTP 429 — never `doi_not_found`, which would assert an absence nothing established

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### `biorxiv_get_fulltext`

Retrieve a preprint's full text as best-effort Markdown.

- Fetches the rendered HTML article page (`www.{server}.org/content/{doi}v{N}.full`) and extracts Markdown — there is no keyless JATS source
- Resolves the latest version via the details API first, for the URL version and clean not-found handling
- Scope to `biorxiv`, `medrxiv`, or `both`; `both` is the default because the two servers share the `10.1101/` DOI prefix. Only the DOI resolution fans out — the full-text fetch targets the single server that answered, named in the output `server` field
- Long articles page via `offset`/`limit` character chunking (`totalChars`, `remainingChars`, `hasMore`); the extracted article is cached per version, so paging costs one origin fetch rather than one per chunk
- PDF-only preprints and blocked/challenge pages return a typed `fulltext_unavailable` error routing to `biorxiv_get_preprint`
- An origin rate limit (HTTP 429) returns a retryable `rate_limited` error carrying the origin's `Retry-After` wait, rather than a bare fetch failure. Both origins this tool touches can hit it — the article page during the full-text fetch, `api.biorxiv.org` during version resolution — and the recovery hint names which of them are limiting, since `biorxiv_get_preprint` is only a useful fallback while the metadata origin is answering

---

### `biorxiv_list_categories`

Return the static subject category taxonomy for both servers.

- No API call — hardcoded static list (~30 bioRxiv + ~50 medRxiv categories)
- Use to validate category strings before passing to `biorxiv_list_recent`

## Features

Built on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core):

- Declarative tool definitions — single file per tool, framework handles registration and validation
- Unified error handling across all tools
- Pluggable auth (`none`, `jwt`, `oauth`)
- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`
- Structured logging with optional OpenTelemetry tracing
- STDIO and Streamable HTTP transports

bioRxiv-specific:

- `BiorxivApiService` wraps `api.biorxiv.org` — details, publications, and crosswalk endpoints with retry and exponential backoff. An origin rate limit (HTTP 429) is classified as a retryable `rate_limited` error carrying the parsed `Retry-After` wait; the upstream response body never reaches the error payload
- `EuropePmcService` wraps the EuropePMC search endpoint for relevance-ranked keyword and/or author results. An origin rate limit (HTTP 429) is classified the same way as the JSON API's — a retryable `rate_limited` error carrying the parsed `Retry-After` wait, with the upstream response body kept out of the error payload
- `BiorxivFullTextService` fetches and extracts Markdown from the rendered HTML article pages on `www.biorxiv.org` / `www.medrxiv.org` — a distinct origin from the JSON API
- Two-server fan-out via `Promise.allSettled` — both `biorxiv` and `medrxiv` queried in parallel when `server