biorxiv-mcp-server

Added value: +{
+  "description": "Preprints whose first version posted on bioRxiv in the interval, for these filters — the rows with version \"1\" across every page of the listing, as bioRxiv counts them. Absent when bioRxiv reports no count, as on an exhausted entry; never a 0 standing in for an unknown count.",
+  "maximum": 9007199254740991,
+  "minimum": -9007199254740991,
+  "type": "integer"
+}

Previous value: -"Total preprints available on bioRxiv for these filters."New value: +"Rows bioRxiv lists in the interval for these filters — one per revision posted in it, so a preprint revised in the interval counts once per version. For the number of new preprints, read newPreprints."

Added value: +{
+  "description": "Preprints whose first version posted on medRxiv in the interval, for these filters — the rows with version \"1\" across every page of the listing, as medRxiv counts them. Absent when medRxiv reports no count, as on an exhausted entry; never a 0 standing in for an unknown count.",
+  "maximum": 9007199254740991,
+  "minimum": -9007199254740991,
+  "type": "integer"
+}

Previous value: -"Total preprints available on medRxiv for these filters."New value: +"Rows medRxiv lists in the interval for these filters — one per revision posted in it, so a preprint revised in the interval counts once per version. For the number of new preprints, read newPreprints."

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."

Previous value: -"Abstract text."New value: +"The preprint's current abstract, present on the latest revision only: api.biorxiv.org keeps one abstract per preprint and repeats it on every revision. For an earlier revision's own abstract, read that revision with biorxiv_get_fulltext and its version input; medRxiv blocks its article pages to some hosts, and there that request fails as fulltext_unavailable."

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

Added value: +[
+  "biorxiv",
+  "medrxiv"
+]

Previous value: -[
-  "doi"
-]New value: +[
+  "doi",
+  "server"
+]

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."

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."

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."

Added value: +{
+  "description": "Journal publisher filter: the DOI prefix its journal articles share, the part before the slash — \"10.7554\" for eLife, \"10.1016\" for Elsevier. Lists only the bioRxiv preprints published under that prefix: medRxiv has no publisher listing, so server=\"both\" queries bioRxiv alone and server=\"medrxiv\" is rejected. Rows listed this way carry no journal name, authors, corresponding author, or abstract.",
+  "pattern": "^10\\.\\d{4,}$",
+  "type": "string"
+}

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_date_range`: start_date or end_date is not a real calendar date (2024-02-30, 2024-13-01), or end_date is before start_date. `upstream_unavailable`: Every attempted server failed against api.biorxiv.org, so no page was retrieved and an empty interval could not be established. `rate_limited`: Every attempted server failed and at least one 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: `invalid_date_range`: start_date or end_date is not a real calendar date (2024-02-30, 2024-13-01), or end_date is before start_date. `invalid_publisher`: publisher is combined with server=\"medrxiv\", or is a prefix api.biorxiv.org does not recognize. `upstream_unavailable`: Every attempted server failed against api.biorxiv.org, so no page was retrieved and an empty interval could not be established. `rate_limited`: Every attempted server failed and at least one was rejected with HTTP 429 by api.biorxiv.org. Other values are possible when a failure originates below the handler."

Previous value: -[
-  "invalid_date_range",
-  "upstream_unavailable",
-  "rate_limited"
-]New value: +[
+  "invalid_date_range",
+  "invalid_publisher",
+  "upstream_unavailable",
+  "rate_limited"
+]

Previous value: -"Guidance on how to read this result set: which servers did not answer, a limit above the 100-row page, which cursors are past the end, which servers have rows past this page, and — when nothing came back — the interval and how to broaden it. All applicable qualifications are composed into one string."New value: +"Guidance on how to read this result set: which servers did not answer, that a publisher filter limited server=\"both\" to bioRxiv and which fields its rows lack, a limit above the 100-row page, which cursors are past the end, which servers have rows past this page, and — when nothing came back — the interval and how to broaden it. All applicable qualifications are composed into one string."

Previous value: -"Preprint abstract. Present only when include_abstract is true."New value: +"Preprint abstract. Present only when include_abstract is true, and never under a publisher filter."

Previous value: -"Corresponding author name."New value: +"Corresponding author name. Absent under a publisher filter."

Previous value: -"Corresponding author institution."New value: +"Corresponding author institution. Absent under a publisher filter."

Previous value: -"Preprint author list."New value: +"Preprint author list. Absent under a publisher filter."

Previous value: -"Name of the publishing journal."New value: +"Name of the publishing journal. Absent under a publisher filter, whose rows carry none."

Added value: +"^\\d{4}-\\d{2}-\\d{2}$"

Added value: +"^\\d{4}-\\d{2}-\\d{2}$"

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_date_range`: end_date is before start_date, or either date is malformed. `invalid_category`: The category is not in the requested server's taxonomy, or api.biorxiv.org ignored it and returned the unfiltered listing on every server that answered. `invalid_funder`: funder is not a well-formed ROR ID (pattern or checksum), is combined with server=\"medrxiv\", or is a ROR ID api.biorxiv.org has no funder record for. `upstream_unavailable`: Every attempted server failed against api.biorxiv.org, so no page was retrieved and an empty interval could not be established. `rate_limited`: Every attempted server failed and at least one 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: `invalid_date_range`: end_date is before start_date, or either date names no calendar day (2024-02-30, 2024-13-01). `invalid_category`: The category is not in the requested server's taxonomy, or api.biorxiv.org ignored it and returned the unfiltered listing on every server that answered. `invalid_funder`: funder is not a well-formed ROR ID (pattern or checksum), is combined with server=\"medrxiv\", or is a ROR ID api.biorxiv.org has no funder record for. `upstream_unavailable`: Every attempted server failed against api.biorxiv.org, so no page was retrieved and an empty interval could not be established. `rate_limited`: Every attempted server failed and at least one was rejected with HTTP 429 by api.biorxiv.org. Other values are possible when a failure originates below the handler."

Previous value: -"Abstract text. Present only when include_abstract is true."New value: +"The preprint's latest-revision abstract, which differs from this row's own revision when a later one exists — api.biorxiv.org keeps one abstract per preprint. Present only when include_abstract is true."

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

Added value: +[
+  "biorxiv",
+  "medrxiv"
+]

Previous value: -[
-  "doi"
-]New value: +[
+  "doi",
+  "server"
+]

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."

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."

Added value: +[
+  "biorxiv",
+  "medrxiv"
+]

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_doi_format`: The input DOI does not match the 10.NNNN/ pattern, even after URL, doi:, and suffix stripping. `version_conflict`: The DOI carries a vN suffix and the version input names a different version. `version_not_found`: The preprint exists but has no revision with the requested version number. `doi_not_found`: The DOI resolves to an empty collection on every attempted server. `upstream_unavailable`: No attempted server resolved the DOI and at least one lookup failed against api.biorxiv.org. `rate_limited`: Either origin returned HTTP 429 for this host — the article page (www.biorxiv.org / www.medrxiv.org) during the full-text fetch, or api.biorxiv.org during version resolution. `fulltext_unavailable`: The preprint exists but its full-text HTML page is blocked, missing, or yields no extractable text (PDF-only). `offset_out_of_range`: offset is greater than or equal to the total character length of the extracted text. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_doi_format`: The input DOI does not match the 10.NNNN/ pattern, even after URL, doi:, and suffix stripping. `version_conflict`: The DOI carries a vN suffix and the version input names a different version. `version_not_found`: The preprint exists but has no revision with the requested version number. `doi_not_found`: The DOI resolves to an empty collection on every attempted server. `upstream_unavailable`: No attempted server resolved the DOI and at least one lookup failed against api.biorxiv.org; the version lookup used most of the call's time budget, so the article page was never requested or had not answered when the budget ran out; or the article page (www.biorxiv.org / www.medrxiv.org) did not answer within the call. `rate_limited`: Either origin returned HTTP 429 for this host — the article page (www.biorxiv.org / www.medrxiv.org) during the full-text fetch, or api.biorxiv.org during version resolution. `fulltext_unavailable`: The preprint exists but its full-text HTML page is blocked, missing, or yields no extractable text (PDF-only). `offset_out_of_range`: offset is greater than or equal to the total character length of the extracted text. Other values are possible when a failure originates below the handler."

Previous value: -"One or more preprint DOIs to look up (max 10)."New value: +"Preprint DOIs to look up, up to 200 entries. The first 10 distinct DOIs are looked up; the rest are returned in unprocessed."

Previous value: -10New value: +200

Previous value: -[
-  {
-    "not": {
-      "required": [
-        "error"
-      ]
-    },
-    "required": [
-      "preprints",
-      "failed"
-    ]
-  },
-  {
-    "required": [
-      "error"
-    ]
-  }
-]New value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "preprints",
+      "failed",
+      "unprocessed"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

Added value: +{
+  "description": "The most distinct DOIs one call looks up.",
+  "type": "number"
+}

Previous value: -"Machine-readable failure mode. Declared by this tool: `doi_not_found`: ALL requested DOIs resolve to empty collections on all requested servers, with every server answering. `invalid_doi_format`: Every input DOI fails to match the 10.NNNN/ pattern, even after URL, doi:, and suffix stripping. `upstream_unavailable`: No DOI resolved and at least one lookup failed against api.biorxiv.org, so absence could not be established for any requested DOI. `rate_limited`: No DOI resolved 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`: Every DOI looked up resolves to empty collections on all requested servers, with every server answering, and no DOI was left in unprocessed. `invalid_doi_format`: Every input entry fails to match the 10.NNNN/ pattern, even after URL, doi:, and suffix stripping. `upstream_unavailable`: No DOI resolved, none was left in unprocessed, and at least one lookup failed against api.biorxiv.org, so absence could not be established for any requested DOI. `rate_limited`: No DOI resolved, none was left in unprocessed, 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."

Added value: +{
+  "description": "How to look up the DOIs left in unprocessed, and how many failed[] entries are retryable alongside them.",
+  "type": "string"
+}

Added value: +{
+  "description": "Distinct DOIs looked up in this call.",
+  "type": "number"
+}

Added value: +{
+  "description": "True when DOIs past the first 10 were left in unprocessed.",
+  "type": "boolean"
+}

Added value: +{
+  "description": "Valid, distinct DOIs past the first 10, in input order — not looked up, so neither found nor failed. Pass this list as dois in another call to continue. Empty when every DOI was looked up.",
+  "items": {
+    "description": "A bare DOI that was not looked up.",
+    "type": "string"
+  },
+  "type": "array"
+}

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."

Previous value: -"Integer row offset (0, 100, 200, …), applied to each queried server. Defaults to 0 (first page)."New value: +"Integer row offset, applied to each queried server. Defaults to 0 (first page). To continue, pass the nextCursor the previous page returned for that server — it advances by the rows actually served."

Added value: +{
+  "default": 25,
+  "description": "Rows to return per queried server, starting at cursor. Defaults to 25. Up to 100, the page api.biorxiv.org serves: a larger value returns 100 rows per server and says so in the notice. limit: 100 walks an interval in the fewest calls.",
+  "maximum": 1000,
+  "minimum": 1,
+  "type": "integer"
+}

Added value: +{
+  "description": "Most publications this page can hold: rows per server (limit, or 100 when limit asked for more) times the servers queried. Set with truncated.",
+  "type": "number"
+}

Previous value: -"Guidance on how to read this result set: which servers did not answer, which cursors are past the end, and — when nothing came back — the interval and how to broaden it. All applicable qualifications are composed into one string."New value: +"Guidance on how to read this result set: which servers did not answer, a limit above the 100-row page, which cursors are past the end, which servers have rows past this page, and — when nothing came back — the interval and how to broaden it. All applicable qualifications are composed into one string."

Previous value: -"Cursor for the next page, when rows remain past this one."New value: +"Cursor for the next page, when rows remain on bioRxiv past this one: this page's cursor plus the rows it served. Pass it as cursor to continue, at any limit."

Previous value: -"Cursor for the next page, when rows remain past this one."New value: +"Cursor for the next page, when rows remain on medRxiv past this one: this page's cursor plus the rows it served. Pass it as cursor to continue, at any limit."

Previous value: -"Date the preprint was first posted (YYYY-MM-DD). Not derivable from the DOI."New value: +"Preprint posting date (YYYY-MM-DD) as this row records it — the first posting for most preprints. medRxiv lists some 10.64898/ preprints on two rows that differ in this date, and sometimes in title or authors; both rows are returned. Not derivable from the DOI."

Added value: +{
+  "description": "Publications on this page, across every server queried. Set with truncated.",
+  "type": "number"
+}

Added value: +{
+  "description": "True when at least one server has rows past this page — continue at that server's nextCursor. Absent when every server queried is on its last page.",
+  "type": "boolean"
+}

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."

Previous value: -100New value: +1000

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

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."

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

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

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"
+}

Previous value: -"Maximum number of characters to return in this chunk. Default 20,000; increase toward 50,000 for large context windows. Check the length field for the actual count returned."New value: +"Maximum number of characters to return in this chunk. Default 20,000; a value past the remaining text returns the rest of the article. Check the length field for the actual count returned."

Previous value: -50000New value: +9007199254740991

Added value: +{
+  "description": "Tables the article page names without their cells — content keeps each one's caption, and the cells live on a separate page at url. The same list on every chunk. Absent when the article has none.",
+  "items": {
+    "additionalProperties": false,
+    "description": "One table whose cells content does not include.",
+    "properties": {
+      "label": {
+        "description": "The table label as the article prints it, e.g. \"Table 1\".",
+        "type": "string"
+      },
+      "url": {
+        "description": "The article origin's page that serves this table's cells. Not fetched by this tool.",
+        "type": "string"
+      }
+    },
+    "required": [
+      "label",
+      "url"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}

Added value: +"^\\d{4}-\\d{2}-\\d{2}$"

Added value: +"^\\d{4}-\\d{2}-\\d{2}$"

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."

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. 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"
+}

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

Added value: +{
+  "description": "Funder filter: the funder's ROR ID, bare (\"021nxhr62\" for the US National Science Foundation) or as a URL (\"https://ror.org/021nxhr62\"). bioRxiv only — medRxiv records carry no funder data, so server=\"both\" queries bioRxiv alone and server=\"medrxiv\" is rejected. Combines with category. Look the ID up by name at ror.org.",
+  "type": "string"
+}

Added value: +{
+  "default": false,
+  "description": "Include each preprint's abstract. Defaults to false: abstracts make up about three quarters of a page, and every other field is returned either way.",
+  "type": "boolean"
+}

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_date_range`: end_date is before start_date, or either date is malformed. `invalid_category`: The category is not in the requested server's taxonomy, or api.biorxiv.org ignored it and returned the unfiltered listing on every server that answered. `upstream_unavailable`: Every attempted server failed against api.biorxiv.org, so no page was retrieved and an empty interval could not be established. `rate_limited`: Every attempted server failed and at least one 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: `invalid_date_range`: end_date is before start_date, or either date is malformed. `invalid_category`: The category is not in the requested server's taxonomy, or api.biorxiv.org ignored it and returned the unfiltered listing on every server that answered. `invalid_funder`: funder is not a well-formed ROR ID (pattern or checksum), is combined with server=\"medrxiv\", or is a ROR ID api.biorxiv.org has no funder record for. `upstream_unavailable`: Every attempted server failed against api.biorxiv.org, so no page was retrieved and an empty interval could not be established. `rate_limited`: Every attempted server failed and at least one was rejected with HTTP 429 by api.biorxiv.org. Other values are possible when a failure originates below the handler."

Previous value: -[
-  "invalid_date_range",
-  "invalid_category",
-  "upstream_unavailable",
-  "rate_limited"
-]New value: +[
+  "invalid_date_range",
+  "invalid_category",
+  "invalid_funder",
+  "upstream_unavailable",
+  "rate_limited"
+]

Previous value: -"Guidance on how to read this result set: which servers did not answer, which ignored the category filter (their unfiltered records are left out), which cursors are past the end, and — when nothing came back — the applied filters and how to broaden them. All applicable qualifications are composed into one string."New value: +"Guidance on how to read this result set: which servers did not answer, which ignored the category filter (their unfiltered records are left out), that a funder filter limited server=\"both\" to bioRxiv, which cursors are past the end, and — when nothing came back — the applied filters and how to broaden them. All applicable qualifications are composed into one string."

Previous value: -"medRxiv pagination state. Present when server is \"medrxiv\" or \"both\"."New value: +"medRxiv pagination state. Present when server is \"medrxiv\" or \"both\", except under a funder filter, which queries bioRxiv only."

Previous value: -"Abstract text."New value: +"Abstract text. Present only when include_abstract is true."

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. 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"
+}

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

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"
+}

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."

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."

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"
+}

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

Previous value: -"Preprint DOI (e.g. 10.1101/2024.05.28.596311 or 10.64898/2026.05.07.723463). The latest version is resolved automatically."New value: +"Preprint DOI (e.g. 10.1101/2024.05.28.596311 or 10.64898/2026.05.07.723463). A doi.org or biorxiv.org/medrxiv.org article URL, a doi: prefix, or a .full suffix is accepted and stripped; a trailing vN (…596311v2) requests that version. Without one, the latest version is resolved automatically."

Added value: +{
+  "description": "Preprint version to read (1, 2, …) — the revision numbers biorxiv_get_preprint lists. Omit for the latest version. Must match a vN suffix on the DOI when both are given.",
+  "maximum": 9007199254740991,
+  "minimum": 1,
+  "type": "integer"
+}

Previous value: -[
-  {
-    "not": {
-      "required": [
-        "error"
-      ]
-    },
-    "required": [
-      "doi",
-      "server",
-      "version",
-      "content",
-      "contentFormat",
-      "sourceUrl",
-      "offset",
-      "length",
-      "totalChars",
-      "remainingChars",
-      "hasMore"
-    ]
-  },
-  {
-    "required": [
-      "error"
-    ]
-  }
-]New value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "doi",
+      "server",
+      "version",
+      "content",
+      "contentFormat",
+      "wordCount",
+      "sourceUrl",
+      "offset",
+      "length",
+      "totalChars",
+      "remainingChars",
+      "hasMore"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_doi_format`: The input DOI does not match the 10.NNNN/ pattern. `doi_not_found`: The DOI resolves to an empty collection on every attempted server. `upstream_unavailable`: No attempted server resolved the DOI and at least one lookup failed against api.biorxiv.org. `rate_limited`: Either origin returned HTTP 429 for this host — the article page (www.biorxiv.org / www.medrxiv.org) during the full-text fetch, or api.biorxiv.org during version resolution. `fulltext_unavailable`: The preprint exists but its full-text HTML page is blocked, missing, or yields no extractable text (PDF-only). `offset_out_of_range`: offset is greater than or equal to the total character length of the extracted text. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `invalid_doi_format`: The input DOI does not match the 10.NNNN/ pattern, even after URL, doi:, and suffix stripping. `version_conflict`: The DOI carries a vN suffix and the version input names a different version. `version_not_found`: The preprint exists but has no revision with the requested version number. `doi_not_found`: The DOI resolves to an empty collection on every attempted server. `upstream_unavailable`: No attempted server resolved the DOI and at least one lookup failed against api.biorxiv.org. `rate_limited`: Either origin returned HTTP 429 for this host — the article page (www.biorxiv.org / www.medrxiv.org) during the full-text fetch, or api.biorxiv.org during version resolution. `fulltext_unavailable`: The preprint exists but its full-text HTML page is blocked, missing, or yields no extractable text (PDF-only). `offset_out_of_range`: offset is greater than or equal to the total character length of the extracted text. Other values are possible when a failure originates below the handler."

Previous value: -[
-  "invalid_doi_format",
-  "doi_not_found",
-  "upstream_unavailable",
-  "rate_limited",
-  "fulltext_unavailable",
-  "offset_out_of_range"
-]New value: +[
+  "invalid_doi_format",
+  "version_conflict",
+  "version_not_found",
+  "doi_not_found",
+  "upstream_unavailable",
+  "rate_limited",
+  "fulltext_unavailable",
+  "offset_out_of_range"
+]

Previous value: -"Preprint version whose full text was retrieved (the latest revision)."New value: +"Preprint version whose full text was retrieved — the requested one, or the latest revision when none was requested. Pass it back as version when paging."

Previous value: -"Approximate word count of the FULL extracted article as reported by the extractor (not just the returned chunk). Absent when the extractor reported none."New value: +"Approximate word count of the FULL extracted article, not just the returned chunk — whitespace-delimited tokens of the same Markdown text that totalChars measures, so Markdown markers such as # and - count too."

Previous value: -"Preprint DOI (e.g. 10.1101/2024.01.15.575123 or 10.64898/2026.05.07.723463)."New value: +"Preprint DOI (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; every revision is returned either way."

Previous value: -"Machine-readable failure mode. Declared by this tool: `doi_not_found`: ALL requested DOIs resolve to empty collections on all requested servers, with every server answering. `invalid_doi_format`: One or more input DOIs do not match the 10.NNNN/ pattern. `upstream_unavailable`: No DOI resolved and at least one lookup failed against api.biorxiv.org, so absence could not be established for any requested DOI. `rate_limited`: No DOI resolved 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`: ALL requested DOIs resolve to empty collections on all requested servers, with every server answering. `invalid_doi_format`: Every input DOI fails to match the 10.NNNN/ pattern, even after URL, doi:, and suffix stripping. `upstream_unavailable`: No DOI resolved and at least one lookup failed against api.biorxiv.org, so absence could not be established for any requested DOI. `rate_limited`: No DOI resolved 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."

Previous value: -"DOI that failed to resolve."New value: +"DOI that failed to resolve — in bare form, or exactly as sent for invalid_doi_format."

Previous value: -"The requested DOI."New value: +"The requested DOI in bare form (any URL, doi: prefix, or suffix removed)."

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."

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."

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"
+}

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

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."

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."

Previous value: -"Subject category filter. Use biorxiv_list_categories for valid values."New value: +"Subject category filter, matched case-insensitively with \"_\" and \"-\" read as a space — \"Cell Biology\", \"cell biology\", \"cell_biology\", and \"cell-biology\" are the same filter. Use biorxiv_list_categories for valid values."

Previous value: -"Machine-readable failure mode. Declared by this tool: `invalid_date_range`: end_date is before start_date, or either date is malformed. `invalid_category`: The supplied category string is not in the taxonomy. `upstream_unavailable`: Every attempted server failed against api.biorxiv.org, so no page was retrieved and an empty interval could not be established. `rate_limited`: Every attempted server failed and at least one 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: `invalid_date_range`: end_date is before start_date, or either date is malformed. `invalid_category`: The category is not in the requested server's taxonomy, or api.biorxiv.org ignored it and returned the unfiltered listing on every server that answered. `upstream_unavailable`: Every attempted server failed against api.biorxiv.org, so no page was retrieved and an empty interval could not be established. `rate_limited`: Every attempted server failed and at least one was rejected with HTTP 429 by api.biorxiv.org. Other values are possible when a failure originates below the handler."

Previous value: -"Guidance on how to read this result set: which servers did not answer, which cursors are past the end, and — when nothing came back — the applied filters and how to broaden them. All applicable qualifications are composed into one string."New value: +"Guidance on how to read this result set: which servers did not answer, which ignored the category filter (their unfiltered records are left out), which cursors are past the end, and — when nothing came back — the applied filters and how to broaden them. All applicable qualifications are composed into one string."

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."

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."

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

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."