Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.
Scored across 11 tools
Most tools have clearly distinct purposes (search, fetch metadata, fetch fulltext, convert IDs, format citations, MeSH lookup, spell check). There is mild overlap between the PubMed and Europe PMC search/fetch pairs, but the descriptions explicitly distinguish corpora and use cases, so an agent can select correctly.
All names use a consistent `pubmed_` prefix with snake_case verb_noun structure. Minor deviation in the two `pubmed_europepmc_*` tools where the source is embedded mid-name rather than as a trailing qualifier, but the pattern remains readable and predictable.
11 tools is well within the sweet spot and each earns its place: search, retrieval, ID conversion, citation handling, related-article discovery, MeSH, and spell check cover distinct needs without redundancy.
The surface covers the full research lifecycle: query with filters, spell-correct, search broad corpora, resolve identifiers, fetch metadata and fulltext, find related/citing works, and format or reverse-lookup citations. No obvious gaps for the stated biomedical-literature purpose.
Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Only resolves articles indexed in PubMed Central — for articles not in PMC, use pubmed_search_articles instead.
| Name | Required | Description | Default |
|---|---|---|---|
| ids | Yes | Article identifiers to convert — one identifier per element, all of the same type. Each element is checked against `idType` before the request: `doi` starts with "10." and carries a "/" ("10.1093/nar/gks1195"); `pmid` is digits ("23193287"); `pmcid` is digits with an optional "PMC" prefix ("PMC3531190" or "3531190"). No element may contain a comma or whitespace — a packed value like "23193287,37952131" is rejected, so split it across elements. | |
| idType | Yes | The type of IDs being submitted. Required so the API can unambiguously resolve them. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| records | No | Conversion results, one per input ID |
| totalConverted | No | Number of IDs successfully converted |
| totalSubmitted | No | Number of IDs submitted |
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 known. The description adds real behavioral context beyond that: the PMC-only resolution boundary and the single-type/50-ID batch constraint. It stops short of describing output or partial-resolution behavior, but that is largely carried by the output schema.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Three short sentences, each earning its place: purpose first, then the batch constraint, then the scope limitation and alternative. No redundancy or filler.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With an output schema present, return values need not be explained, and the description supplies the key operational facts an agent needs: what it converts, batch limits, and the PMC-indexing boundary plus the fallback tool. Nothing essential for correct invocation is missing.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, and the schema already documents the ID formats, the 50-item cap, and single-type requirement in far more detail than the description. The description's parameter mentions ('up to 50 IDs of a single type') merely restate constraints already fully specified, so the baseline 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
States a specific verb ('Convert') and resource ('article identifiers (DOI, PMID, PMCID)'), making the tool's function unambiguous. It also signals scope via the PMC-only note, so an agent can distinguish it from the search/fetch siblings.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly names a when-not condition ('Only resolves articles indexed in PubMed Central') and routes the agent to the correct alternative for those cases ('use pubmed_search_articles instead'). It also states the per-request limit of 50 single-type IDs.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Fetch complete Europe PMC records — including the full, untruncated abstract — addressed as records: [{ source, epmcId }], an array even for one record. Pairs with pubmed_europepmc_search, which returns bounded abstractSnippet values and flags cut ones with abstractTruncated: true; copy each hit's source and epmcId into records here to read the whole abstract. This is the retrieval path for preprint (PPR), patent (PAT), and Agricola (AGR) records, which frequently carry no PMID and no DOI, so pubmed_fetch_articles and pubmed_fetch_fulltext cannot address them. Up to 25 records per call. Set maxResponseCharacters to bound the whole response: records past the ceiling are deferred whole and listed in deferred.records for a follow-up call.
| Name | Required | Description | Default |
|---|---|---|---|
| records | Yes | Records to retrieve, each addressed by the `source` and `epmcId` of a `pubmed_europepmc_search` hit. The whole batch resolves in one Europe PMC request. | |
| maxResponseCharacters | No | Opt-in ceiling for the whole response, in characters. Each record is measured as the JSON record it is returned as — title, authors, journal, abstract, identifiers, every field it carries. Records are kept in the order Europe PMC returned them until the next one would cross the ceiling; that record and the rest are deferred whole (never partially populated) and listed in `deferred.records`. Response envelope fields — `notFound`, `deferred` itself — are not counted. Omit to return every resolved record. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| notice | No | Guidance when one or more requested records could not be resolved, or when `maxResponseCharacters` deferred records — naming how to retrieve them. Absent when every requested record came back. |
| records | No | Resolved records, in the order Europe PMC returned them. Under a `maxResponseCharacters` budget, only the leading records that fit; `deferred.records` lists the rest. |
| deferred | No | Continuation state for records the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one record. |
| notFound | No | Requested `source` + `epmcId` pairs Europe PMC returned no record for. Reported in full regardless of where a `maxResponseCharacters` cut lands — these are misses, not deferrals. |
| truncated | No | True when `maxResponseCharacters` withheld at least one resolved record. Absent when the response carries every record that resolved. The continuation state is in `deferred`. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations only declare readOnly and openWorld; the description adds substantial behavior beyond that: a 25-record batch ceiling, single-request resolution, and precise truncation semantics (records deferred whole, never partially populated, listed in deferred.records, envelope fields uncounted). This is exactly the extra context annotations do not carry.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Front-loaded with the core action and the full-abstract payoff, then the pairing workflow, then the batch limit and ceiling behavior. Some parenthetical detail is dense, but every sentence carries distinct information and nothing is padding.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With an output schema present, the description need not explain return fields, yet it still clarifies the deferred.records envelope behavior. Batch limits, addressing format, and sibling routing are all covered for a two-parameter retrieval tool.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100% and the schema already documents source/epmcId and maxResponseCharacters thoroughly, so the baseline is 3. The description adds value by stressing the array-form requirement even for a single record and by restating the deferral behavior of maxResponseCharacters in workflow terms.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
States a specific verb and resource ('Fetch complete Europe PMC records — including the full, untruncated abstract') and immediately distinguishes itself from pubmed_europepmc_search, pubmed_fetch_articles, and pubmed_fetch_fulltext. An agent can tell exactly what this retrieves and what it does not.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Names the sibling to pair with, explains the workflow (copy source and epmcId from search hits), and gives the exclusion case explicitly: PPR/PAT/AGR records have no PMID/DOI so the other fetch tools cannot address them. When-to-use and when-not-to-use are both covered.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (source: PPR), patents (source: PAT), Agricola (source: AGR), plus everything in PubMed (MED) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via cursorMark. Defaults to MED, PMC, and PPR; pass sources to include PAT / AGR. Abstracts arrive as a bounded abstractSnippet with abstractTruncated marking the cut ones — pass a hit to pubmed_europepmc_fetch as records: [{ source, epmcId }] for the complete abstract.
| Name | Required | Description | Default |
|---|---|---|---|
| sort | No | Optional EPMC sort: `<field> asc|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year), `FIRST_IDATE_D` (date first indexed in Europe PMC). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking; `relevance` or `relevance desc` is sent as no sort. Field and direction match case-insensitively. Each key must be one field plus `asc` or `desc`: a key without a direction, an empty key, or an extra word fails with `europepmc_invalid_input` before the request. A field outside the documented set may be honored, silently ignored, or refused — a sort Europe PMC refuses fails with `europepmc_invalid_input` naming it, and an empty Europe PMC response to a sort with an undocumented field fails the same way, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: ["PPR"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR desc` to order preprints by date. | |
| query | Yes | Europe PMC search query. Supports field tokens like `AUTH:"<name>"`, `JOURNAL:"<title>"`, `TITLE:"<words>"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:"..."`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens may be quoted or unquoted — this tool wraps every query with its `sources` filter, and Europe PMC honors a quoted identifier inside that wrapper. A PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`, whichever identifier is used. Free text is matched broadly across abstract/title/keywords. A query with no search term — blank once HTML entities are decoded and markup, parentheses, and invisible characters are disregarded, such as `()` or `<b></b>` — is rejected; any other query is sent as written. | |
| sources | No | Filter to specific EPMC sources. Defaults to MED, PMC, PPR when omitted. Pass an explicit array including PAT or AGR to broaden coverage. Allowed values: MED, PMC, PPR, PAT, AGR. | |
| pageSize | No | Results per page. Max 100 per EPMC API. | |
| cursorMark | No | Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` verbatim for subsequent pages. A whitespace-only cursor, invisible characters included, is rejected before the request, and a cursor Europe PMC cannot read fails with `europepmc_invalid_input` once a retry of it fails again while the first page of the same query is served. | * |
| resultType | No | `core` returns abstract, IDs, dates, license; `lite` is a smaller payload with IDs and titles only. | core |
| Name | Required | Description |
|---|---|---|
| hits | No | Matching Europe PMC records, in the order EPMC returned them |
| error | No | Present when the call failed. Absent on success. |
| query | No | Effective query string echoed by Europe PMC |
| notice | No | Optional guidance when results are empty or paging overshot |
| searchUrl | No | Europe PMC's website search URL for this query |
| cursorMark | No | Cursor used for this response (echoed from the request) |
| totalCount | No | Total matching records across all pages |
| appliedSources | No | Sources the query was filtered against (defaults applied) |
| nextCursorMark | No | Cursor to pass back as `cursorMark` for the next page. Absent on the final page. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations only cover readOnlyHint/openWorldHint, so the safety profile is done; the description adds real behavioral context beyond that: the default source scoping (MED/PMC/PPR), cursorMark pagination, and notably that abstracts arrive truncated as a bounded abstractSnippet flagged by abstractTruncated. That truncation quirk is exactly the kind of trait annotations cannot express.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Front-loaded with what the corpus is and when to reach for it, then pagination and the truncation caveat. Dense and mostly waste-free, though the heavy inline-code syntax makes it longer than it needs to be.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With an output schema present, return values need no explanation; the description still covers corpus scope, default/explicit source selection, pagination, truncation handling, and the handoff to pubmed_europepmc_fetch. Nothing an agent needs to call it correctly is missing.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100% and the schema is unusually detailed (sort semantics, error cases, enum values), so the parameter baseline is 3. The description largely repeats schema facts — default sources, cursorMark pagination — and adds only the routing hint of passing { source, epmcId } to the fetch tool.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
States a specific verb and resource ('Search Europe PMC, a broad open-access biomedical corpus') and enumerates the distinct source families (PPR, PAT, AGR, MED, PMC) that set it apart from the PubMed-only sibling pubmed_search_articles. An agent can distinguish it from siblings without opening a schema.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Gives an explicit selection rule: 'Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery.' It also names pubmed_europepmc_fetch as the follow-up for full abstracts. It stops short of explicitly naming the alternative search tool to use otherwise, so it is clear context rather than full when/when-not routing.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms, and linked retraction, erratum, and comment notices; grants and the members of a collective author are opt-in (includeGrants, includeInvestigators). Set maxResponseCharacters to bound the whole response: articles past the ceiling are deferred whole and listed in deferred.ids for a follow-up call.
| Name | Required | Description | Default |
|---|---|---|---|
| pmids | Yes | PubMed IDs to fetch | |
| includeMesh | No | Include MeSH terms | |
| includeGrants | No | Include grant information | |
| includeInvestigators | No | Include `investigators`: the members NCBI lists for a collective author such as "TGU Investigators". Off by default because the list is unbounded: consortium trials name thousands, at about 60 characters of JSON each — PMID 33933206 lists 6,349, adding about 372,000 characters to its record. Under `maxResponseCharacters` they count toward the size of their article, which is deferred whole when it no longer fits. | |
| maxResponseCharacters | No | Opt-in ceiling for the whole response, in characters. Each article is measured as the JSON record it is returned as — title, abstract, authors, journal, MeSH terms, grants, identifiers, every field it carries. Articles are kept in response order until the next one would cross the ceiling; that article and the rest are deferred whole (never partially populated) and listed in `deferred.ids`. Response envelope fields — counts, `unavailablePmids`, `deferred` itself — are not counted. Omit to return every resolved article. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| notice | No | Optional guidance when no articles were returned — points to discovery tools — or when `maxResponseCharacters` deferred articles, naming how to retrieve them. Absent on successful unbudgeted fetches. |
| articles | No | Parsed articles |
| deferred | No | Continuation state for articles the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one article. |
| truncated | No | True when `maxResponseCharacters` withheld at least one resolved article. Absent when the response carries every article that resolved. The continuation state is in `deferred`. |
| totalReturned | No | Number of articles in this response. Under a `maxResponseCharacters` budget this counts the kept articles only; `deferred.deferredCount` covers the rest. |
| unavailablePmids | No | PMIDs PubMed returned no record for. That is all this reports: PubMed omits an unknown PMID silently, with no error and no reason, so the absence says nothing about whether the PMID exists. Reported in full regardless of where a `maxResponseCharacters` cutoff lands — these are misses, not deferrals. Use `pubmed_search_articles` to find PMIDs that do resolve. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Beyond readOnlyHint/openWorldHint the description discloses real operational behavior: opt-in semantics and defaults for grants/investigators, why investigators is off (unbounded list, thousands of members), and the exact truncation contract (articles measured as full JSON records, deferred whole rather than partially populated, envelope fields excluded from the count).
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Two sentences, front-loaded with the primary action and return payload, then the opt-ins and the ceiling behavior. No filler, and the truncation contract is stated compactly enough to be actionable.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With an output schema present and annotations covering the safety profile, the description only needs to supply behavior the structured fields cannot: opt-in defaults and the deferral/ceiling contract. Those are all present, and return-value detail is rightly left to the output schema.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100% and the property descriptions already explain includeInvestigators and maxResponseCharacters in depth, so the description largely restates structured data. Baseline 3 is appropriate; it adds framing about the ceiling but no new parameter syntax or formats.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
States a specific verb and resource (fetch full article metadata by PubMed IDs) and enumerates the payload (abstract, authors, journal, MeSH terms, notices), which implicitly separates it from pubmed_fetch_fulltext. It never names a sibling, so an agent must infer the boundary with pubmed_search_articles/pubmed_fetch_fulltext rather than being told.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Usage is only implied: fetch by known IDs, and issue a follow-up call for ids listed in deferred.ids. There is no explicit statement of when to prefer this over pubmed_fetch_fulltext or how it pairs with pubmed_search_articles, and no exclusion guidance.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Fetch full-text articles from PubMed Central as structured sections — the body, then back matter such as acknowledgments, declarations, and appendices — with tables and references. When PMC misses, transparently falls back to Europe PMC fullTextXML (structured JATS for records with a PMC counterpart), then to Unpaywall — publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text. Name articles by pmcids (PMC IDs directly), pmids (PubMed IDs, auto-resolved), dois (DOIs, auto-resolved to PMC via the ID Converter; preprints and EPMC-only OA fall through to the Europe PMC and Unpaywall layers), or any mix of the three — up to 50 distinct identifiers; the first 10 are fetched per call, the rest returned in overLimit; an article several of them name is fetched and returned once. Two independent character controls: maxCharacters caps body text per article, maxResponseCharacters caps the whole response and defers articles past the ceiling whole, listing them in deferred.ids for a follow-up call.
| Name | Required | Description | Default |
|---|---|---|---|
| dois | No | DOIs to resolve (e.g. ["10.21203/rs.3.rs-9010375/v1"]), one per element. Combinable with `pmcids` and `pmids` — up to 50 distinct identifiers across the three; the first 10 are fetched per call, the rest returned in `overLimit`. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled. | |
| pmids | No | PubMed IDs. Combinable with `pmcids` and `dois` — up to 50 distinct identifiers across the three; the first 10 are fetched per call, the rest returned in `overLimit`. Articles in PMC are returned as structured JATS; articles not in PMC fall through to Europe PMC (when EPMC has a `fullTextXML`), then to Unpaywall when `UNPAYWALL_EMAIL` is set and a DOI is available. | |
| pmcids | No | PMC IDs to fetch (e.g. ["PMC9575052"]). Combinable with `pmids` and `dois` — up to 50 distinct identifiers across the three; the first 10 are fetched per call, the rest returned in `overLimit`. PMC IDs with no retrievable full text fall through to Europe PMC, then to Unpaywall on the DOI the chain resolves for them. | |
| sections | No | Filter to specific sections by title (e.g. ["Introduction", "Methods", "Results", "Discussion"]). A term matches a section or subsection title at any nesting depth, case-insensitively, as a substring — "resul" matches "Results". Back-matter sections match the same way: by their own titles, or by their kind when they carry neither a title nor a label — "appendix" matches a section titled "Appendix A", "footnotes" an untitled footnote group. A label is never matched, so an appendix labelled "Appendix A" under a title of its own matches only on that title. A section whose own title matches is returned whole; one kept only because a nested subsection matched keeps its heading as a breadcrumb, with its own text cleared and only the matching branch beneath it. Tables and assets narrow with the filter: one whose section did not survive, or that names no section, is dropped. Empty strings are skipped, so `[""]` applies no filter; an element of only whitespace or invisible characters, such as a zero-width space, is rejected. Applies to `source=pmc` results only. | |
| maxSections | No | Maximum top-level sections. Back-matter sections count and follow the body, so a cap drops them first. Applies to `source=pmc` results only. | |
| overflowMode | No | How to spend `maxCharacters` across an article that exceeds it. truncate: fill sections in document order, so early sections stay whole, the section the budget runs out in is cut, and every section or subsection past that point is dropped (counted in `truncation.omittedSections`). outline: split the budget evenly so every section and subsection keeps its heading, and an excerpt as far as the budget reaches — a heading the budget left empty is marked as such in the rendered text. In both modes the body sections spend the budget first and back-matter sections share what the body, tables, and assets leave. Use it to survey what an article contains before requesting specific `sections`. Ignored when no budget is set, and identical for `source=unpaywall` bodies, which have no headings to preserve. | truncate |
| includeAssets | No | Include the article's figures and supplementary material — `assets[]`, each with its label, caption, enclosing section and deposit pointer. On by default because it is cheaper than tables: a median asset-bearing article grows about 10%, and the body prose already refers to these by label. Set false to omit them, which also removes the `[Figure: …]` / `[Supplementary: …]` markers from the section text, since without the array they point at nothing. Prose-shaped blocks — lists, definition lists, block quotes, boxed text, preformatted blocks, displayed formulae — are section text rather than assets and this switch never affects them. Applies to `source=pmc` results only. | |
| includeTables | No | Include the article's tables — cells, captions, labels and footnotes. On by default because a dropped table takes its numbers with it. Table-dense articles pay for it: rendered tables typically add 12–17% to an article record and can more than double it. Set false to omit them, or cap the cost with `maxCharacters`, which drops tables it cannot fit whole. Applies to `source=pmc` results only. | |
| maxCharacters | No | Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text — which carries the inline blocks the parser renders in place, such as lists, definition lists, block quotes, boxed text, preformatted blocks and displayed formulae — plus table label, caption, cell and footnote text and asset label, caption and `href` text; or the `source=unpaywall` `content` body. Titles, abstracts, identifiers, and references are never counted or shortened. Shortened text ends at the last word boundary inside its allowance, so it can come back a few characters under it. The counted unit is that text alone — the Markdown grid `content[]` renders around the cells (pipes, padding, the divider row, headings) is scaffolding this budget does not measure, so a table renders longer than it costs here. Body sections are served first, then tables, then assets, then back-matter sections, each spending what is left, in document order. For tables and assets, admission stops at the first entry that does not fit, and every entry from there on is dropped whole rather than cut mid-row or returned with a shortened caption, counted in `truncation.omittedTables` / `truncation.omittedAssets` and named in `truncation.articles[].omittedTableNames` / `omittedAssetNames`. Back matter takes only what remains and is shortened or dropped as body sections are; `sections` still returns it after the body. Applied after `sections`, `maxSections`, `includeReferences`, `includeTables`, and `includeAssets`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body. | |
| includeReferences | No | Include reference list. Applies to `source=pmc` results only. | |
| maxResponseCharacters | No | Opt-in ceiling for the whole response, in characters — the true response-wide counterpart to the per-article `maxCharacters`. Each article is measured as the JSON record it is returned as, after every filter and the per-article body budget: title, abstract, sections, references, identifiers, license and source metadata — every field it carries. One ledger covers all tiers, so PMC-, Europe PMC-, and Unpaywall-served articles spend the same budget. Articles are kept in the order `articles` lists them until the next one would cross the ceiling; that article and the rest are deferred whole (never partially populated) and listed in `deferred.ids`. Response envelope fields — counts, `unavailable`, `truncation`, `deferred` itself — are not counted. Omit to return every resolved article. | |
| maxCharactersPerSection | No | Budget for a single top-level section, in characters, counting the section text plus its subsections. Combine with `maxCharacters` to cap both one section and the article; the tighter of the two wins. Applies to `source=pmc` results only. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| notice | No | Optional guidance for a partial or empty body. A `sections`-filter miss names the requested terms and affected article id(s) and suggests retrying without `sections` or using broader headings. A metadata-only record names the id(s) the chain could retrieve as front matter only and points at `pubmed_fetch_articles` for the abstract. A table returned with no cell values names the affected table(s), the article each came from, and why the cells cannot be recovered. A budgeted response names the characters returned versus carried and points at `truncation`. A response-wide budget that deferred articles names the ids to re-request. Identifiers past the per-call limit are named with the field to resend each under. Absent when none of those applies. |
| articles | No | Full-text articles in routing order — `pmcids`, then `pmids`, then `dois`, request order within each — each at the position of the id it would be deferred under, whichever tier served it. An article several ids name appears once. |
| deferred | No | Continuation state for articles the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one article. |
| overLimit | No | Identifiers the call named past the per-call fetch limit, returned unfetched for a follow-up call. Present only when the call named more than `limit` distinct identifiers. Separate from `deferred`, which lists articles that were fetched but withheld by `maxResponseCharacters`. |
| truncated | No | True when a character budget shortened at least one returned body or withheld a whole article, or when the call named more distinct identifiers than one call fetches. Absent when every requested identifier was fetched and every resolved article is present with its full post-filter body. The per-article body accounting is in `truncation`; the withheld ids are in `deferred`; the unfetched ids are in `overLimit`. |
| truncation | No | Character accounting for full text the budget shortened. Present only when a budget actually removed characters — its absence means every returned article carries its full post-filter body. |
| unavailable | No | Per-identifier explanations for any requested PMIDs, PMCIDs, or DOIs with no returnable full text. `idType` names the field each id was sent in. Distinct from `deferred`: nothing here is retrievable by re-calling, and an id never appears in both. Ids past the per-call limit are listed in `overLimit`, never here. |
| totalReturned | No | Number of articles in this response. Under a `maxResponseCharacters` budget this counts the kept articles only; `deferred.deferredCount` covers the rest. |
Get formatted citations for PubMed articles in one or more formats (apa, mla, bibtex, ris, vancouver). Pass a single format as a string or multiple as an array. Retractions, errata, and expressions of concern NCBI links to an article come back in notices; Vancouver and APA also cite a retraction in the reference itself.
| Name | Required | Description | Default |
|---|---|---|---|
| pmids | Yes | PubMed IDs to cite | |
| format | No | Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris, vancouver. | apa |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| notice | No | Optional guidance when no citations were produced — points to discovery tools. Absent when at least one citation was produced. |
| citations | No | Citations per article |
| totalFormatted | No | Number of PMIDs successfully formatted |
| totalSubmitted | No | Number of PMIDs submitted for citation formatting |
| unavailablePmids | No | PMIDs PubMed returned no record for, so nothing could be cited for them. That is all this reports: PubMed omits a PMID it does not recognize silently, with no error and no reason, so the absence says nothing about whether the PMID exists. Use `pubmed_search_articles` to find PMIDs that do resolve. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint=true and openWorldHint=true, so safety is covered. The description adds genuinely useful behavior beyond that: retractions, errata, and expressions of concern come back in `notices`, and Vancouver/APA also cite a retraction inline in the reference itself — a non-obvious output trait the agent would not learn from the schema.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Three sentences, purpose front-loaded, no filler, and the unusual `notices` behavior is placed last where it is easy to skim. The middle sentence largely duplicates the schema's anyOf constraint, which is the only mild waste.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With an output schema present, the description need not explain return values, and it correctly focuses on formats and the retraction-notice behavior. It is complete enough to call correctly, though it omits any note about the 50-PMID cap or failure behavior for invalid IDs.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100% and both parameters are fully documented in the schema, including the allowed style values and the string-or-array anyOf. The description restates the same single-vs-array rule and the same style list without adding syntax, defaults, or ordering semantics, so baseline 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description states a specific verb and resource ('Get formatted citations for PubMed articles') and enumerates the supported styles, so the tool's function is unmistakable. It does not, however, distinguish itself from siblings such as pubmed_lookup_citation or pubmed_fetch_articles, which an agent may confuse it with when choosing a tool.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Usage is only implied: the agent can infer it should call this when it needs citations in a given style, and the string-vs-array note hints at how to request multiple styles. There is no explicit when-to-use versus alternatives guidance, no mention of the sibling pubmed_lookup_citation, and no stated limits or prerequisites.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or a four-digit year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.
| Name | Required | Description | Default |
|---|---|---|---|
| citations | Yes | Citations to look up, 1–25, each matched independently. More fields = better match accuracy. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| results | No | Match results, one per input citation |
| totalMatched | No | Number of citations with PMID matches |
| totalWarnings | No | Number of matched citations that carry at least one warning |
| totalSubmitted | No | Number of citations submitted |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations only cover readOnlyHint and openWorldHint, so the description carries most of the behavioral load and does so well: it discloses the ECitMatch primary-key rule (journal+volume+page), that author-only or volume-only inputs guarantee no match, and that richer input improves match accuracy. It does not mention the 1–25 batch cap (left to the schema) or any rate/limit behavior, but the added matching semantics are substantial.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Three sentences, front-loaded with the purpose before the constraints, and each sentence carries information. Minor redundancy with the schema's own item description ('more fields = better match accuracy' appears in both), which keeps it from a 5.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
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 need not be explained, and annotations cover the safety profile. Combined with the required-field constraint, the no-match failure mode, and the accuracy heuristic, an agent has everything needed to build a valid call.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
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 above that by adding the accuracy heuristic ('more fields = better match accuracy') and the failure-mode rule that journal or a four-digit year is mandatory. Some of this overlaps the nested schema description, but the match-accuracy guidance is genuinely additional.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
States a specific verb and resource ('Look up PubMed IDs from partial bibliographic citations') and pins down the exact input shape (journal, year, volume, page, author). It implicitly separates itself from free-text search siblings by calling the matching 'deterministic' and contrasting it with 'free-text search for structured references'.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Gives a clear trigger: use it when you already hold a structured reference and need the PMID, and explicitly says it beats free-text search for structured references. It does not name the alternative sibling tool (e.g., pubmed_search_articles) or state when not to reach for this one, which keeps it short of a 5.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms, plus pagination via offset for paging past the maxResults cap.
| Name | Required | Description | Default |
|---|---|---|---|
| query | Yes | MeSH descriptor name or free-text term to look up. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than searched. | |
| offset | No | Result offset for pagination (0-based). Pass the `nextOffset` from the previous response to get the following page; the exact-descriptor match is pinned to the first page only. | |
| maxResults | No | Maximum results | |
| includeDetails | No | Fetch full MeSH records (scope notes, tree numbers, entry terms) |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| query | No | Original search query |
| notice | No | Optional guidance when no descriptors matched or the offset overshot the result set — suggests spell-check, free-text search, or resetting the offset. Absent on successful result pages. |
| offset | No | Result offset this page was read from |
| results | No | Matching MeSH records |
| nextOffset | No | Offset to request for the next page. Omitted when this is the last page, so its absence is the end-of-results signal. |
| totalCount | No | Total MeSH descriptors matching the query upstream, before the maxResults cap |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint=true and openWorldHint=true, so safety is covered. The description adds genuine behavioral context beyond that: the shape of the returned descriptor records (tree numbers, scope notes, entry terms) and the pagination model for paging past the maxResults cap.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Two sentences, zero filler, with the purpose front-loaded ahead of the return/pagination detail. Nothing is repeated or padding, though the second sentence is a dense clause stack rather than cleanly separated points.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a read-only lookup tool with a fully documented schema and an output schema covering return values, the description supplies enough to call it correctly. It needn't explain the record fields in detail since the output schema exists, though it does so anyway.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, so the schema already documents all four parameters, including offset's nextOffset chaining and the whitespace-rejection rule for query. The description only adds a brief mention of offset-based paging, which is already in the schema, so baseline 3 applies.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description gives a specific verb pair (search/explore) and a precise resource (the MeSH controlled vocabulary), which is inherently distinguishable from the article-oriented siblings like pubmed_search_articles and pubmed_find_related. It does not explicitly name an alternative, but the resource itself separates it cleanly from every sibling.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Usage is implied rather than stated: an agent can infer it should call this when it needs MeSH descriptor data, but the description never says when to prefer it over pubmed_search_articles or pubmed_spell_check, nor any prerequisite for looking up a descriptor. Adequate but with a clear gap.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), and pagination via offset for paging through large result sets.
| Name | Required | Description | Default |
|---|---|---|---|
| sort | No | Sort order: relevance (default), pub_date (newest first), author, or journal | relevance |
| query | Yes | PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup, bracketed field tags (`[pdat]`), parentheses, and invisible characters such as a zero-width space are disregarded is rejected rather than sent to PubMed. | |
| author | No | Filter by author name (e.g. "Smith J"). An empty string applies no filter; a value of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected. | |
| offset | No | Result offset for pagination (0-based). PubMed serves at most the first 9999 records of a result set, so this caps at 9998; narrow the query or add filters to reach anything beyond it. | |
| journal | No | Filter by journal name. An empty string applies no filter; a value of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected. | |
| species | No | Filter by species | |
| language | No | Filter by language (e.g. "english"). An empty string applies no filter; a value of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected. | |
| dateRange | No | Filter by date range. The filter is applied only when both `minDate` and `maxDate` are non-empty; either one empty disables the entire date range. A partial date covers its whole year or month, and a range whose `minDate` falls after its `maxDate` is rejected: `2024/06` to `2024` is valid, `2024/07` to `2024/06/30` is not. | |
| meshTerms | No | Filter by MeSH terms. Multiple terms are AND'd — all must match. Empty strings are skipped; an element of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected. | |
| maxResults | No | Maximum results to return. 0 returns only `totalCount`. | |
| hasAbstract | No | Only include articles with abstracts | |
| freeFullText | No | Only include free full text articles | |
| summaryCount | No | Fetch brief summaries for top N results (0 = PMIDs only). Above the 50 cap, pass the remaining PMIDs to pubmed_fetch_articles. | |
| publicationTypes | No | Filter by publication type (e.g. "Review", "Clinical Trial", "Meta-Analysis"). Multiple values are OR'd — any match qualifies. Empty strings are skipped; an element of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| pmids | No | PubMed IDs |
| query | No | Original query |
| notice | No | Optional guidance when the result set does not reflect what was asked for — a field tag PubMed ignored, a phrase it matched nothing for, a dateRange dropped for having one bound, no matches at all, or paging past the end. Absent when nothing applies. |
| offset | No | Result offset used |
| searchUrl | No | PubMed search URL |
| summaries | No | Brief summaries (empty array when summaryCount is 0) |
| totalCount | No | Total matching articles |
| appliedFilters | No | Normalized filter values that were applied to the PubMed query |
| effectiveQuery | No | Sanitized query sent to PubMed after applying all active filters |
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. The description adds the return shape (PMIDs, optional brief summaries) and the paging mechanism, but says nothing about result caps, rate limits, or the 9999-record ceiling that constrains paging.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Three sentences, front-loaded with the core action and return value, then filters, then pagination. No filler, though the filter enumeration is partly redundant with the schema.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
With an output schema present, return-value detail isn't required, and 14 parameters are fully documented in the schema. The description supplies a coherent capability overview, leaving only sibling routing unaddressed.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
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 groups the filters (field-specific: author/journal/MeSH; common: language/species/free full text) which matches the schema but adds no syntax, default, or edge-case detail beyond it.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
States a specific verb+resource ("Search PubMed") and scopes the capability set (query syntax, filters, date ranges, returned PMIDs/summaries). It does not explicitly contrast itself with the close sibling pubmed_europepmc_search, so an agent must infer which backend to pick, but the purpose itself is unmistakable.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description notes pagination via offset "for paging through large result sets," which is mild usage guidance, but it never says when to choose this tool over pubmed_europepmc_search, pubmed_find_related, or pubmed_fetch_articles. The only sibling redirect (fetch_articles above the summary cap) lives in the schema, not the description.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Spell-check a PubMed search query against NCBI ESpell and get the corrected query back. Use after a zero-hit or thin pubmed_search_articles result, or when a drug, gene, disease, or author name may be misspelled. Corrections are applied in place, so field tags, operators, spacing, and gene symbols stay as written (alzhiemer diseese treatmnt outcomse → alzheimer disease treatment outcomes). Words in all capitals, with digits or non-ASCII letters, or differing only in case are never changed, words after a number or symbol ESpell skips are left as written, and hasSuggestion is false when no correction was applied. Re-run the search with corrected.
| Name | Required | Description | Default |
|---|---|---|---|
| query | Yes | PubMed search query to spell-check. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than sent to ESpell. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| original | No | Original query |
| corrected | No | The query with ESpell's accepted corrections applied in place; field tags, operators, spacing, and words in capitals or with digits are kept as written. Same as `original` when `hasSuggestion` is false. |
| hasSuggestion | No | Whether at least one correction was applied to `corrected` |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations only declare readOnlyHint and openWorldHint, but the description discloses real behavioral detail: corrections are applied in place preserving tags/operators/spacing, capitals and digit/non-ASCII tokens are never altered, tokens after numbers or symbols ESpell skips are left as written, and hasSuggestion is false when nothing changed. This is unusually rich context beyond the structured fields.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Purpose and trigger are front-loaded in the first two sentences, which is exactly right. The middle sentence is dense and packs many edge-case rules into one breath, but every clause conveys actionable behavior, so nothing is wasted.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
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 need not be enumerated; the description instead supplies the one output field agents must key on (hasSuggestion) and the corrected payload to re-use. For a single-parameter read tool, nothing an agent needs to call it correctly is missing.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100% and the single query parameter is fully documented in the schema, including the whitespace/zero-width rejection rule. The description adds the illustrative example ('alzhiemer diseese treatmnt outcomse') but no syntax or format information beyond what the schema already carries, so baseline 3 applies.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Names a specific verb and resource ('Spell-check a PubMed search query') and the backend ('NCBI ESpell'), plus the outcome ('get the corrected query back'). It is immediately distinguishable from siblings like pubmed_search_articles or pubmed_lookup_mesh 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.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Explicitly names the trigger condition and the sibling to check ('Use after a zero-hit or thin pubmed_search_articles result') plus a second scenario ('when a drug, gene, disease, or author name may be misspelled'). It even tells the agent the follow-up action ('Re-run the search with corrected'), closing the loop.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
pubmed_europepmc_fetch2 fields changedOutput schema / properties / deferred / properties / nextDeferredCharacters / descriptionPrevious value: -"Serialized size of the next deferred record — the first entry in `records`, where the response stopped. Raise `maxResponseCharacters` to at least this to make progress; a smaller record further down `records` cannot be reached until this one fits."New value: +"Serialized size of the next deferred record — the first entry in `records`, where the response stopped — and the continuation ceiling: re-calling with the deferred pairs needs `maxResponseCharacters` ≥ this to return anything, and a smaller record further down `records` cannot be reached until this one fits. Repeating this same call needs `maxResponseCharacters` ≥ `returnedCharacters` + this to return this record as well."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message in place of results; a sort it cannot use (one whose keys are not each a field plus asc/desc, rejected before any request; an empty response to a sort with an undocumented field; or a second HTTP 503 to a sorted search when the same query without the sort is served); or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."pubmed_europepmc_search4 fields changedInput schema / properties / sort / descriptionPrevious value: -"Optional EPMC sort: `<field> asc|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Field and direction match case-insensitively. A field outside the documented set may be honored, silently ignored, or rejected, and a sort using one — or a key without `asc`/`desc` — can fail with `europepmc_invalid_input` naming it, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: [\"PPR\"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date."New value: +"Optional EPMC sort: `<field> asc|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year), `FIRST_IDATE_D` (date first indexed in Europe PMC). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking; `relevance` or `relevance desc` is sent as no sort. Field and direction match case-insensitively. Each key must be one field plus `asc` or `desc`: a key without a direction, an empty key, or an extra word fails with `europepmc_invalid_input` before the request. A field outside the documented set may be honored, silently ignored, or refused — a sort Europe PMC refuses fails with `europepmc_invalid_input` naming it, and an empty Europe PMC response to a sort with an undocumented field fails the same way, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: [\"PPR\"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR desc` to order preprints by date."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served). `blank_query`: The query contains no search term: nothing is left once whitespace and invisible characters such as a zero-width space are disregarded. pubmed_search_articles and pubmed_europepmc_search first decode HTML entities and also disregard markup and parentheses, so `()`, `<b></b>`, and ` ` hold no term there; pubmed_search_articles also disregards bracketed field tags such as `[pdat]`. `blank_cursor`: The `cursorMark` holds only whitespace or invisible characters such as a zero-width space. Europe PMC cannot read it and answers with the HTTP 503 it also uses for an outage. `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message in place of results; a sort it cannot use (one whose keys are not each a field plus asc/desc, rejected before any request; an empty response to a sort with an undocumented field; or a second HTTP 503 to a sorted search when the same query without the sort is served); or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served). `blank_query`: The query contains no search term: nothing is left once whitespace and invisible characters such as a zero-width space are disregarded. pubmed_search_articles and pubmed_europepmc_search first decode HTML entities and also disregard markup and parentheses, so `()`, `<b></b>`, and ` ` hold no term there; pubmed_search_articles also disregards bracketed field tags such as `[pdat]`. `blank_cursor`: The `cursorMark` holds only whitespace or invisible characters such as a zero-width space. Europe PMC cannot read it and answers with the HTTP 503 it also uses for an outage. `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."Output schema / properties / hits / items / properties / abstractTruncated / descriptionPrevious value: -"Whether `abstractSnippet` was cut short of the full abstract. Retrieve the complete text with `pubmed_europepmc_fetch` using this record’s `source` and `epmcId`. Present whenever `abstractSnippet` is; omitted when Europe PMC carries no abstract."New value: +"Whether `abstractSnippet` was cut short of the full abstract. Retrieve the complete text by passing this record to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]`. Present whenever `abstractSnippet` is; omitted when Europe PMC carries no abstract."Output schema / properties / hits / items / properties / epmcId / descriptionPrevious value: -"Europe PMC's internal record id. Pass it with this hit's `source` to `pubmed_europepmc_fetch` for the complete record. Europe PMC's `fullTextXML` is keyed on `pmcId`, not on this id, so records without a PMC counterpart have no full text to fetch."New value: +"Europe PMC's internal record id. Pass it with this hit's `source` to `pubmed_europepmc_fetch` as `records: [{ source, epmcId }]` for the complete record. Europe PMC's `fullTextXML` is keyed on `pmcId`, not on this id, so records without a PMC counterpart have no full text to fetch."pubmed_fetch_articles4 fields changedOutput schema / properties / articles / items / properties / authors / items / properties / suffixAdded value: +{
+ "description": "Generational name suffix verbatim from NCBI `Suffix` (e.g. \"Jr\", \"2nd\", \"3rd\"), never normalized. Absent when NCBI gives none.",
+ "type": "string"
+}Output schema / properties / articles / items / properties / book / properties / editors / items / properties / suffixAdded value: +{
+ "description": "Editor generational name suffix verbatim from NCBI `Suffix` (e.g. \"Jr\"). Absent when NCBI supplies none, or on a group editor.",
+ "type": "string"
+}Output schema / properties / articles / items / properties / investigators / items / properties / suffixAdded value: +{
+ "description": "Generational name suffix verbatim from NCBI `Suffix` (e.g. \"Jr\", \"2nd\"). Absent when NCBI gives none.",
+ "type": "string"
+}Output schema / properties / deferred / properties / nextDeferredCharacters / descriptionPrevious value: -"Serialized size of the next deferred article — the first entry in `ids`, where the response stopped. Raise `maxResponseCharacters` to at least this to make progress; a smaller article further down `ids` cannot be reached until this one fits."New value: +"Serialized size of the next deferred article — the first entry in `ids`, where the response stopped — and the continuation ceiling: re-calling with the deferred PMIDs needs `maxResponseCharacters` ≥ this to return anything, and a smaller article further down `ids` cannot be reached until this one fits. Repeating this same call needs `maxResponseCharacters` ≥ `returnedCharacters` + this to return this article as well."pubmed_fetch_fulltext9 fields changedInput schema / properties / maxResponseCharacters / descriptionPrevious value: -"Opt-in ceiling for the whole response, in characters — the true response-wide counterpart to the per-article `maxCharacters`. Each article is measured as the JSON record it is returned as, after every filter and the per-article body budget: title, abstract, sections, references, identifiers, license and source metadata — every field it carries. One ledger covers all tiers, so PMC-, Europe PMC-, and Unpaywall-served articles spend the same budget. Articles are kept in response order until the next one would cross the ceiling; that article and the rest are deferred whole (never partially populated) and listed in `deferred.ids`. Response envelope fields — counts, `unavailable`, `truncation`, `deferred` itself — are not counted. Omit to return every resolved article."New value: +"Opt-in ceiling for the whole response, in characters — the true response-wide counterpart to the per-article `maxCharacters`. Each article is measured as the JSON record it is returned as, after every filter and the per-article body budget: title, abstract, sections, references, identifiers, license and source metadata — every field it carries. One ledger covers all tiers, so PMC-, Europe PMC-, and Unpaywall-served articles spend the same budget. Articles are kept in the order `articles` lists them until the next one would cross the ceiling; that article and the rest are deferred whole (never partially populated) and listed in `deferred.ids`. Response envelope fields — counts, `unavailable`, `truncation`, `deferred` itself — are not counted. Omit to return every resolved article."Output schema / properties / articles / descriptionPrevious value: -"Full-text articles"New value: +"Full-text articles in routing order — `pmcids`, then `pmids`, then `dois`, request order within each — each at the position of the id it would be deferred under, whichever tier served it. An article several ids name appears once."Output schema / properties / articles / items / oneOfPrevious value: -[
- {
- "additionalProperties": false,
- "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
- "properties": {
- "abstract": {
- "description": "Abstract",
- "type": "string"
- },
- "affiliations": {
- "description": "Author affiliations",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "articleType": {
- "description": "Article type",
- "type": "string"
- },
- "assets": {
- "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from a section, body or back matter, leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One figure or supplementary-material item, with its caption, pointer, and section",
- "properties": {
- "assetType": {
- "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
- "enum": [
- "figure",
- "supplementary-material"
- ],
- "type": "string"
- },
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "href": {
- "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
- "type": "string"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Display label as printed, e.g. `Fig. 1`",
- "type": "string"
- },
- "sectionTitle": {
- "description": "Title of the innermost titled section enclosing the asset — a body section or a back-matter one such as an appendix — as that section is titled in `sections`, or, for a heading nested deeper than `sections` carries, as its heading line inside the text of the section that contains it. Absent for an asset inside no titled section, such as a `<floats-group>` deposit.",
- "type": "string"
- }
- },
- "required": [
- "assetType"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "authors": {
- "description": "Authors",
- "items": {
- "additionalProperties": false,
- "description": "Author entry",
- "properties": {
- "collectiveName": {
- "description": "Group name",
- "type": "string"
- },
- "givenNames": {
- "description": "Given names",
- "type": "string"
- },
- "lastName": {
- "description": "Last name",
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "doi": {
- "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
- "type": "string"
- },
- "epmcId": {
- "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
- "type": "string"
- },
- "epmcSource": {
- "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
- "type": "string"
- },
- "journal": {
- "additionalProperties": false,
- "description": "Journal information",
- "properties": {
- "elocationId": {
- "description": "Electronic article locator from JATS `<elocation-id>` — the publisher-assigned article number (e.g. \"e20542\"). Journals that assign article numbers deposit no `<fpage>`, so this is the only locator on roughly half of PMC records. Never a substitute for `pages`; JATS carries no type attribute, so there is no counterpart to the `elocationIdType` that `pubmed_fetch_articles` reports.",
- "type": "string"
- },
- "issn": {
- "description": "ISSN",
- "type": "string"
- },
- "issue": {
- "description": "Issue number",
- "type": "string"
- },
- "pages": {
- "description": "Page range",
- "type": "string"
- },
- "title": {
- "description": "Journal title",
- "type": "string"
- },
- "volume": {
- "description": "Volume number",
- "type": "string"
- }
- },
- "type": "object"
- },
- "keywords": {
- "description": "Keywords",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "pmcId": {
- "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
- "type": "string"
- },
- "pmcUrl": {
- "description": "PMC URL — derived from `pmcId` when present",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID",
- "type": "string"
- },
- "publicationDate": {
- "additionalProperties": false,
- "description": "Publication date",
- "properties": {
- "day": {
- "description": "Publication day",
- "type": "string"
- },
- "month": {
- "description": "Publication month",
- "type": "string"
- },
- "year": {
- "description": "Publication year",
- "type": "string"
- }
- },
- "type": "object"
- },
- "pubmedUrl": {
- "description": "PubMed URL",
- "type": "string"
- },
- "references": {
- "description": "Reference list",
- "items": {
- "additionalProperties": false,
- "description": "Reference entry",
- "properties": {
- "citation": {
- "description": "Citation text",
- "type": "string"
- },
- "id": {
- "description": "Reference ID",
- "type": "string"
- },
- "label": {
- "description": "Reference label",
- "type": "string"
- }
- },
- "required": [
- "citation"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "sections": {
- "description": "Article sections in source order: the body, then the back matter — acknowledgments, notes and declarations, footnotes, glossary, appendices. A back-matter element with no heading of its own is titled by its kind, such as `Footnotes` or `Appendix`.",
- "items": {
- "additionalProperties": false,
- "description": "Article section, from the body or from the back matter after it",
- "properties": {
- "label": {
- "description": "Section label",
- "type": "string"
- },
- "subsections": {
- "description": "Nested subsections",
- "items": {
- "additionalProperties": false,
- "description": "Article subsection",
- "properties": {
- "label": {
- "description": "Subsection label",
- "type": "string"
- },
- "text": {
- "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
- "type": "string"
- },
- "title": {
- "description": "Subsection heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "text": {
- "description": "Section body text",
- "type": "string"
- },
- "title": {
- "description": "Section heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "source": {
- "const": "pmc",
- "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
- "type": "string"
- },
- "tables": {
- "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One table from the article, with its cells, caption, and owning section",
- "properties": {
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "footnotes": {
- "description": "`<table-wrap-foot>` text, one line per footnote or paragraph, joined by `\\n`. A footnote marker deposited as a `<label>` leads its line, followed by a space (`* No patient …`).",
- "type": "string"
- },
- "headerRowCount": {
- "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
- "type": "number"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Table label as printed, e.g. `TABLE 1`",
- "type": "string"
- },
- "rows": {
- "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. A line break in a cell — a `<break/>`, a paragraph, or a list item in the source — is kept as `\\n`, so `1.08\\n2.44` is two values; superscripts and other inline markup are never spaced (`0.108a`). Empty when `unextractableReason` is set.",
- "items": {
- "description": "One row, as cell text by grid column",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "type": "array"
- },
- "sectionTitle": {
- "description": "Title of the innermost titled section enclosing the table — a body section or a back-matter one such as an appendix — as that section is titled in `sections`, or, for a heading nested deeper than `sections` carries, as its heading line inside the text of the section that contains it. A `sections` filter keeps the table with that section. In back matter the section name is the only positional cue there is. Absent for a table inside no titled section, such as a `<floats-group>` deposit.",
- "type": "string"
- },
- "unextractableReason": {
- "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
- "enum": [
- "cals-tgroup",
- "graphic-only",
- "no-rows"
- ],
- "type": "string"
- }
- },
- "required": [
- "headerRowCount",
- "rows"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "title": {
- "description": "Article title",
- "type": "string"
- },
- "viaSource": {
- "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
- "enum": [
- "pmc",
- "europepmc"
- ],
- "type": "string"
- }
- },
- "required": [
- "source",
- "viaSource",
- "sections"
- ],
- "type": "object"
- },
- {
- "additionalProperties": false,
- "description": "Best-effort full text from an open-access copy",
- "properties": {
- "content": {
- "description": "Full article text — Markdown or plain text per `contentFormat`",
- "type": "string"
- },
- "contentFormat": {
- "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
- "enum": [
- "html-markdown",
- "pdf-text"
- ],
- "type": "string"
- },
- "doi": {
- "description": "DOI used to locate the open-access copy",
- "type": "string"
- },
- "hostType": {
- "description": "`publisher` or `repository` — where the OA copy is hosted",
- "type": "string"
- },
- "journalName": {
- "description": "Journal or repository name from Unpaywall's record for the DOI (e.g. `medRxiv` for a medRxiv preprint). Absent when Unpaywall has none.",
- "type": "string"
- },
- "license": {
- "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
- "type": "string"
- },
- "pmcId": {
- "description": "PMC ID this article was requested under, in `PMC<digits>` form — present when a `pmcids` entry named it, absent when it was requested under a PMID or DOI. When several identifiers name one article, it is requested under the first to reach it: `pmcids`, then `pmids`, then `dois`. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID this article was requested under — present when it was requested under a `pmids` entry, absent when under a PMC ID or DOI (see `pmcId` for which identifier an article several of them name is requested under)",
- "type": "string"
- },
- "pubmedUrl": {
- "description": "PubMed URL — present when `pmid` is set",
- "type": "string"
- },
- "source": {
- "const": "unpaywall",
- "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
- "type": "string"
- },
- "sourceUrl": {
- "description": "URL the content was fetched from",
- "type": "string"
- },
- "title": {
- "description": "Article title, from the first source that carries one: Unpaywall's record for the DOI, then the Europe PMC record when the chain searched Europe PMC for this id, then — for `html-markdown` content only — the title detected on the page. Absent when none of them has a title.",
- "type": "string"
- },
- "totalPages": {
- "description": "Page count reported by the PDF extractor; absent for HTML",
- "type": "number"
- },
- "version": {
- "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
- "type": "string"
- },
- "viaSource": {
- "const": "unpaywall",
- "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
- "type": "string"
- },
- "wordCount": {
- "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
- "type": "number"
- },
- "year": {
- "description": "Publication year from Unpaywall's record for the DOI. Absent when Unpaywall has none.",
- "type": "number"
- }
- },
- "required": [
- "source",
- "viaSource",
- "contentFormat",
- "doi",
- "sourceUrl",
- "content"
- ],
- "type": "object"
- }
-]New value: +[
+ {
+ "additionalProperties": false,
+ "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
+ "properties": {
+ "abstract": {
+ "description": "Abstract",
+ "type": "string"
+ },
+ "affiliations": {
+ "description": "Author affiliations",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "articleType": {
+ "description": "Article type",
+ "type": "string"
+ },
+ "assets": {
+ "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from a section, body or back matter, leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One figure or supplementary-material item, with its caption, pointer, and section",
+ "properties": {
+ "assetType": {
+ "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
+ "enum": [
+ "figure",
+ "supplementary-material"
+ ],
+ "type": "string"
+ },
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "href": {
+ "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
+ "type": "string"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Display label as printed, e.g. `Fig. 1`, less one trailing ` |`, `.` or `:` (`Figure 1.` reads `Figure 1`). Some supplements carry a bare number (`1`), kept as deposited here",
+ "type": "string"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost titled section enclosing the asset — a body section or a back-matter one such as an appendix — as that section is titled in `sections`, or, for a heading nested deeper than `sections` carries, as its heading line inside the text of the section that contains it. Absent for an asset inside no titled section, such as a `<floats-group>` deposit.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "assetType"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "authors": {
+ "description": "Authors",
+ "items": {
+ "additionalProperties": false,
+ "description": "Author entry",
+ "properties": {
+ "collectiveName": {
+ "description": "Group name",
+ "type": "string"
+ },
+ "givenNames": {
+ "description": "Given names",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Last name",
+ "type": "string"
+ },
+ "suffix": {
+ "description": "Generational name suffix verbatim from the JATS `<suffix>` (e.g. \"Jr\", \"IV\"), never normalized. Absent when the deposit gives none.",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "doi": {
+ "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
+ "type": "string"
+ },
+ "epmcId": {
+ "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
+ "type": "string"
+ },
+ "epmcSource": {
+ "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
+ "type": "string"
+ },
+ "journal": {
+ "additionalProperties": false,
+ "description": "Journal information",
+ "properties": {
+ "elocationId": {
+ "description": "Electronic article locator from JATS `<elocation-id>` — the publisher-assigned article number (e.g. \"e20542\"). Journals that assign article numbers deposit no `<fpage>`, so this is the only locator on roughly half of PMC records. Never a substitute for `pages`; JATS carries no type attribute, so there is no counterpart to the `elocationIdType` that `pubmed_fetch_articles` reports.",
+ "type": "string"
+ },
+ "issn": {
+ "description": "ISSN",
+ "type": "string"
+ },
+ "issue": {
+ "description": "Issue number",
+ "type": "string"
+ },
+ "pages": {
+ "description": "Page range",
+ "type": "string"
+ },
+ "title": {
+ "description": "Journal title",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "keywords": {
+ "description": "Keywords",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "pmcId": {
+ "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
+ "type": "string"
+ },
+ "pmcUrl": {
+ "description": "PMC URL — derived from `pmcId` when present",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID",
+ "type": "string"
+ },
+ "publicationDate": {
+ "additionalProperties": false,
+ "description": "Publication date",
+ "properties": {
+ "day": {
+ "description": "Publication day",
+ "type": "string"
+ },
+ "month": {
+ "description": "Publication month",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL",
+ "type": "string"
+ },
+ "references": {
+ "description": "Reference list",
+ "items": {
+ "additionalProperties": false,
+ "description": "Reference entry",
+ "properties": {
+ "citation": {
+ "description": "Citation text",
+ "type": "string"
+ },
+ "id": {
+ "description": "Reference ID",
+ "type": "string"
+ },
+ "label": {
+ "description": "Reference label",
+ "type": "string"
+ }
+ },
+ "required": [
+ "citation"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "sections": {
+ "description": "Article sections in source order: the body, then the back matter — acknowledgments, notes and declarations, footnotes, glossary, appendices. A back-matter element with no heading of its own is titled by its kind, such as `Footnotes` or `Appendix`.",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article section, from the body or from the back matter after it",
+ "properties": {
+ "label": {
+ "description": "Section label",
+ "type": "string"
+ },
+ "subsections": {
+ "description": "Nested subsections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article subsection",
+ "properties": {
+ "label": {
+ "description": "Subsection label",
+ "type": "string"
+ },
+ "text": {
+ "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
+ "type": "string"
+ },
+ "title": {
+ "description": "Subsection heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "text": {
+ "description": "Section body text",
+ "type": "string"
+ },
+ "title": {
+ "description": "Section heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "source": {
+ "const": "pmc",
+ "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
+ "type": "string"
+ },
+ "tables": {
+ "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One table from the article, with its cells, caption, and owning section",
+ "properties": {
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "footnotes": {
+ "description": "`<table-wrap-foot>` text, one line per footnote or paragraph, joined by `\\n`. A footnote marker deposited as a `<label>` leads its line, followed by a space (`* No patient …`).",
+ "type": "string"
+ },
+ "headerRowCount": {
+ "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
+ "type": "number"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Table label as printed, e.g. `TABLE 1`, less one trailing ` |`, `.` or `:` (`Table 1.` reads `Table 1`)",
+ "type": "string"
+ },
+ "rows": {
+ "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. A line break in a cell — a `<break/>`, a paragraph, or a list item in the source — is kept as `\\n`, so `1.08\\n2.44` is two values; superscripts and other inline markup are never spaced (`0.108a`). Empty when `unextractableReason` is set.",
+ "items": {
+ "description": "One row, as cell text by grid column",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "type": "array"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost titled section enclosing the table — a body section or a back-matter one such as an appendix — as that section is titled in `sections`, or, for a heading nested deeper than `sections` carries, as its heading line inside the text of the section that contains it. A `sections` filter keeps the table with that section. In back matter the section name is the only positional cue there is. Absent for a table inside no titled section, such as a `<floats-group>` deposit.",
+ "type": "string"
+ },
+ "unextractableReason": {
+ "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
+ "enum": [
+ "cals-tgroup",
+ "graphic-only",
+ "no-rows"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "headerRowCount",
+ "rows"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "title": {
+ "description": "Article title",
+ "type": "string"
+ },
+ "viaSource": {
+ "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
+ "enum": [
+ "pmc",
+ "europepmc"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "sections"
+ ],
+ "type": "object"
+ },
+ {
+ "additionalProperties": false,
+ "description": "Best-effort full text from an open-access copy",
+ "properties": {
+ "content": {
+ "description": "Full article text — Markdown or plain text per `contentFormat`",
+ "type": "string"
+ },
+ "contentFormat": {
+ "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
+ "enum": [
+ "html-markdown",
+ "pdf-text"
+ ],
+ "type": "string"
+ },
+ "doi": {
+ "description": "DOI used to locate the open-access copy",
+ "type": "string"
+ },
+ "hostType": {
+ "description": "`publisher` or `repository` — where the OA copy is hosted",
+ "type": "string"
+ },
+ "journalName": {
+ "description": "Journal or repository name from Unpaywall's record for the DOI (e.g. `medRxiv` for a medRxiv preprint). Absent when Unpaywall has none.",
+ "type": "string"
+ },
+ "license": {
+ "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
+ "type": "string"
+ },
+ "pmcId": {
+ "description": "PMC ID this article was requested under, in `PMC<digits>` form — present when a `pmcids` entry named it, absent when it was requested under a PMID or DOI. When several identifiers name one article, it is requested under the first to reach it: `pmcids`, then `pmids`, then `dois`. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID this article was requested under — present when it was requested under a `pmids` entry, absent when under a PMC ID or DOI (see `pmcId` for which identifier an article several of them name is requested under)",
+ "type": "string"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL — present when `pmid` is set",
+ "type": "string"
+ },
+ "source": {
+ "const": "unpaywall",
+ "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
+ "type": "string"
+ },
+ "sourceUrl": {
+ "description": "URL the content was fetched from",
+ "type": "string"
+ },
+ "title": {
+ "description": "Article title, from the first source that carries one: Unpaywall's record for the DOI, then the Europe PMC record when the chain searched Europe PMC for this id, then — for `html-markdown` content only — the title detected on the page. Absent when none of them has a title.",
+ "type": "string"
+ },
+ "totalPages": {
+ "description": "Page count reported by the PDF extractor; absent for HTML",
+ "type": "number"
+ },
+ "version": {
+ "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
+ "type": "string"
+ },
+ "viaSource": {
+ "const": "unpaywall",
+ "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
+ "type": "string"
+ },
+ "wordCount": {
+ "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
+ "type": "number"
+ },
+ "year": {
+ "description": "Publication year from Unpaywall's record for the DOI. Absent when Unpaywall has none.",
+ "type": "number"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "contentFormat",
+ "doi",
+ "sourceUrl",
+ "content"
+ ],
+ "type": "object"
+ }
+]Output schema / properties / deferred / properties / dois / descriptionPrevious value: -"The deferred ids sent as DOIs, in response order — re-submit them as `dois`. Present only when the deferred ids came from more than one field (so `idType` is absent) and one of them was a DOI."New value: +"The deferred ids sent as DOIs, in routing order — re-submit them as `dois`. Present only when the deferred ids came from more than one field (so `idType` is absent) and one of them was a DOI."Output schema / properties / deferred / properties / ids / descriptionPrevious value: -"Identifiers of the deferred articles, in response order, keyed as they were requested (PMC IDs in `PMC<digits>` form). Re-call `pubmed_fetch_fulltext` with these under the `idType` field — or, when `idType` is absent, with the `pmcids` / `pmids` / `dois` lists below — and the same other inputs. Never contains an id from `unavailable`."New value: +"Identifiers of the deferred articles, in routing order — `pmcids`, then `pmids`, then `dois`, request order within each — keyed as they were requested (PMC IDs in `PMC<digits>` form). Re-call `pubmed_fetch_fulltext` with these under the `idType` field — or, when `idType` is absent, with the `pmcids` / `pmids` / `dois` lists below — and the same other inputs. Never contains an id from `unavailable`."Output schema / properties / deferred / properties / nextDeferredCharacters / descriptionPrevious value: -"Serialized size of the next deferred article — the first entry in `ids`, where the response stopped. Raise `maxResponseCharacters` to at least this to make progress; a smaller article further down `ids` cannot be reached until this one fits."New value: +"Serialized size of the next deferred article — the first entry in `ids`, where the response stopped — and the continuation ceiling: re-calling with the deferred ids needs `maxResponseCharacters` ≥ this to return anything, and a smaller article further down `ids` cannot be reached until this one fits. Repeating this same call needs `maxResponseCharacters` ≥ `returnedCharacters` + this to return this article as well."Output schema / properties / deferred / properties / pmcids / descriptionPrevious value: -"The deferred ids sent as PMC IDs, in response order — re-submit them as `pmcids`. Present only when the deferred ids came from more than one field (so `idType` is absent) and one of them was a PMC ID."New value: +"The deferred ids sent as PMC IDs, in routing order — re-submit them as `pmcids`. Present only when the deferred ids came from more than one field (so `idType` is absent) and one of them was a PMC ID."Output schema / properties / deferred / properties / pmids / descriptionPrevious value: -"The deferred ids sent as PMIDs, in response order — re-submit them as `pmids`. Present only when the deferred ids came from more than one field (so `idType` is absent) and one of them was a PMID."New value: +"The deferred ids sent as PMIDs, in routing order — re-submit them as `pmids`. Present only when the deferred ids came from more than one field (so `idType` is absent) and one of them was a PMID."Output schema / properties / truncation / properties / articles / items / properties / omittedAssetNames / descriptionPrevious value: -"The dropped assets by name, in document order — each asset's label, else its `id`, else `asset <n>` for its position in the article. Contiguous for the same reason `omittedTableNames` is: admission stops at the first asset that did not fit rather than skipping ahead to a smaller one. Absent when none were dropped."New value: +"The dropped assets by name, in document order — each asset's label (a bare-number label led by its type, `Supplementary material 1`), else its `id`, else `asset <n>` for its position in the article. Contiguous for the same reason `omittedTableNames` is: admission stops at the first asset that did not fit rather than skipping ahead to a smaller one. Absent when none were dropped."pubmed_lookup_mesh3 fields changedOutput schema / properties / results / items / properties / meshId / descriptionPrevious value: -"Canonical MeSH DescriptorUI (e.g. \"D003924\") — resolves at the MeSH Browser and NLM linked data. Falls back to the raw Entrez UID when a record is not decodable."New value: +"Canonical MeSH unique identifier (e.g. \"D003924\", \"C000626284\", \"Q000009\") — resolves at the MeSH Browser and NLM linked data. A pharmacological-action record carries its descriptor's UI. Omitted only when eSummary returned no record for this UID."Output schema / properties / results / items / properties / treeNumbers / descriptionPrevious value: -"Navigable MeSH tree numbers (e.g. \"D02.078.370.141.450\"). Omitted for supplementary concept records (SCRs), which map to a heading rather than occupying a tree position."New value: +"Navigable MeSH tree numbers (e.g. \"D02.078.370.141.450\"). Omitted for supplementary concept records (SCRs), which map to a heading rather than occupying a tree position, and for pharmacological-action records, whose descriptor carries the tree positions."Output schema / properties / results / items / requiredPrevious value: -[
- "meshId",
- "entrezUid",
- "name"
-]New value: +[
+ "entrezUid",
+ "name"
+]pubmed_spell_check2 fields changedOutput schema / properties / corrected / descriptionPrevious value: -"Corrected query (same as original if no suggestion)"New value: +"The query with ESpell's accepted corrections applied in place; field tags, operators, spacing, and words in capitals or with digits are kept as written. Same as `original` when `hasSuggestion` is false."Output schema / properties / hasSuggestion / descriptionPrevious value: -"Whether NCBI suggested a correction"New value: +"Whether at least one correction was applied to `corrected`"pubmed_europepmc_fetch1 field changedInput schema / properties / maxResponseCharacters / maximumPrevious value: -1000000New value: +9007199254740991pubmed_fetch_articles5 fields changedInput schema / properties / includeInvestigatorsAdded value: +{
+ "default": false,
+ "description": "Include `investigators`: the members NCBI lists for a collective author such as \"TGU Investigators\". Off by default because the list is unbounded: consortium trials name thousands, at about 60 characters of JSON each — PMID 33933206 lists 6,349, adding about 372,000 characters to its record. Under `maxResponseCharacters` they count toward the size of their article, which is deferred whole when it no longer fits.",
+ "type": "boolean"
+}Input schema / properties / maxResponseCharacters / maximumPrevious value: -1000000New value: +9007199254740991Output schema / properties / articles / items / properties / affiliations / descriptionPrevious value: -"Deduplicated author affiliations"New value: +"Deduplicated affiliations, referenced by `affiliationIndices`: the authors' entries first, then any that only `investigators` carry"Output schema / properties / articles / items / properties / authors / items / properties / collectiveName / descriptionPrevious value: -"Group/collective author name"New value: +"Group/collective author name. NCBI may list the members of the group separately; set `includeInvestigators` to return them as `investigators`."Output schema / properties / articles / items / properties / investigatorsAdded value: +{
+ "description": "Members of the article's collective author, from NCBI's `InvestigatorList`: every list flattened in NCBI's order, uncapped. They are not authors, and no citation style lists them. Present only when `includeInvestigators` is set and the record lists any; never on `book-chapter` or `book` records.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One member of a collective author, from NCBI's `InvestigatorList`",
+ "properties": {
+ "affiliationIndices": {
+ "description": "Indices into the top-level affiliations array, where an investigator's affiliations follow the authors'",
+ "items": {
+ "type": "number"
+ },
+ "type": "array"
+ },
+ "firstName": {
+ "description": "First/given name",
+ "type": "string"
+ },
+ "initials": {
+ "description": "Initials",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Last name",
+ "type": "string"
+ },
+ "orcid": {
+ "description": "ORCID identifier",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+}pubmed_fetch_fulltext25 fields changedInput schema / properties / dois / descriptionPrevious value: -"DOIs to resolve (e.g. [\"10.21203/rs.3.rs-9010375/v1\"]), one per element. Combinable with `pmcids` and `pmids` — at most 10 distinct identifiers across the three. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled."New value: +"DOIs to resolve (e.g. [\"10.21203/rs.3.rs-9010375/v1\"]), one per element. Combinable with `pmcids` and `pmids` — up to 50 distinct identifiers across the three; the first 10 are fetched per call, the rest returned in `overLimit`. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled."Input schema / properties / dois / maxItemsPrevious value: -10New value: +50Input schema / properties / maxCharacters / descriptionPrevious value: -"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text — which carries the inline blocks the parser renders in place, such as lists, definition lists, block quotes, boxed text, preformatted blocks and displayed formulae — plus table label, caption, cell and footnote text and asset label, caption and `href` text; or the `source=unpaywall` `content` body. Titles, abstracts, identifiers, and references are never counted or shortened. Shortened text ends at the last word boundary inside its allowance, so it can come back a few characters under it. The counted unit is that text alone — the Markdown grid `content[]` renders around the cells (pipes, padding, the divider row, headings) is scaffolding this budget does not measure, so a table renders longer than it costs here. Sections are served first, then tables, then assets, each spending what is left, in document order — admission stops at the first entry that does not fit, and every entry from there on is dropped whole rather than cut mid-row or returned with a shortened caption, counted in `truncation.omittedTables` / `truncation.omittedAssets` and named in `truncation.articles[].omittedTableNames` / `omittedAssetNames`. Applied after `sections`, `maxSections`, `includeReferences`, `includeTables`, and `includeAssets`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body."New value: +"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text — which carries the inline blocks the parser renders in place, such as lists, definition lists, block quotes, boxed text, preformatted blocks and displayed formulae — plus table label, caption, cell and footnote text and asset label, caption and `href` text; or the `source=unpaywall` `content` body. Titles, abstracts, identifiers, and references are never counted or shortened. Shortened text ends at the last word boundary inside its allowance, so it can come back a few characters under it. The counted unit is that text alone — the Markdown grid `content[]` renders around the cells (pipes, padding, the divider row, headings) is scaffolding this budget does not measure, so a table renders longer than it costs here. Body sections are served first, then tables, then assets, then back-matter sections, each spending what is left, in document order. For tables and assets, admission stops at the first entry that does not fit, and every entry from there on is dropped whole rather than cut mid-row or returned with a shortened caption, counted in `truncation.omittedTables` / `truncation.omittedAssets` and named in `truncation.articles[].omittedTableNames` / `omittedAssetNames`. Back matter takes only what remains and is shortened or dropped as body sections are; `sections` still returns it after the body. Applied after `sections`, `maxSections`, `includeReferences`, `includeTables`, and `includeAssets`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body."Input schema / properties / maxCharacters / maximumPrevious value: -1000000New value: +9007199254740991Input schema / properties / maxCharactersPerSection / descriptionPrevious value: -"Budget for a single top-level body section, in characters, counting the section text plus its subsections. Combine with `maxCharacters` to cap both one section and the article; the tighter of the two wins. Applies to `source=pmc` results only."New value: +"Budget for a single top-level section, in characters, counting the section text plus its subsections. Combine with `maxCharacters` to cap both one section and the article; the tighter of the two wins. Applies to `source=pmc` results only."Input schema / properties / maxCharactersPerSection / maximumPrevious value: -1000000New value: +9007199254740991Input schema / properties / maxResponseCharacters / descriptionPrevious value: -"Opt-in ceiling for the whole response, in characters — the true response-wide counterpart to the per-article `maxCharacters`. Each article is measured as the JSON record it is returned as, after every filter and the per-article body budget: title, abstract, body sections, references, identifiers, license and source metadata — every field it carries. One ledger covers all tiers, so PMC-, Europe PMC-, and Unpaywall-served articles spend the same budget. Articles are kept in response order until the next one would cross the ceiling; that article and the rest are deferred whole (never partially populated) and listed in `deferred.ids`. Response envelope fields — counts, `unavailable`, `truncation`, `deferred` itself — are not counted. Omit to return every resolved article."New value: +"Opt-in ceiling for the whole response, in characters — the true response-wide counterpart to the per-article `maxCharacters`. Each article is measured as the JSON record it is returned as, after every filter and the per-article body budget: title, abstract, sections, references, identifiers, license and source metadata — every field it carries. One ledger covers all tiers, so PMC-, Europe PMC-, and Unpaywall-served articles spend the same budget. Articles are kept in response order until the next one would cross the ceiling; that article and the rest are deferred whole (never partially populated) and listed in `deferred.ids`. Response envelope fields — counts, `unavailable`, `truncation`, `deferred` itself — are not counted. Omit to return every resolved article."Input schema / properties / maxResponseCharacters / maximumPrevious value: -1000000New value: +9007199254740991Input schema / properties / maxSections / descriptionPrevious value: -"Maximum top-level body sections. Applies to `source=pmc` results only."New value: +"Maximum top-level sections. Back-matter sections count and follow the body, so a cap drops them first. Applies to `source=pmc` results only."Input schema / properties / maxSections / maximumPrevious value: -50New value: +9007199254740991Input schema / properties / overflowMode / descriptionPrevious value: -"How to spend `maxCharacters` across an article that exceeds it. truncate: fill sections in document order, so early sections stay whole, the section the budget runs out in is cut, and every section or subsection past that point is dropped (counted in `truncation.omittedSections`). outline: split the budget evenly so every section and subsection keeps its heading, and an excerpt as far as the budget reaches — a heading the budget left empty is marked as such in the rendered text. Use it to survey what an article contains before requesting specific `sections`. Ignored when no budget is set, and identical for `source=unpaywall` bodies, which have no headings to preserve."New value: +"How to spend `maxCharacters` across an article that exceeds it. truncate: fill sections in document order, so early sections stay whole, the section the budget runs out in is cut, and every section or subsection past that point is dropped (counted in `truncation.omittedSections`). outline: split the budget evenly so every section and subsection keeps its heading, and an excerpt as far as the budget reaches — a heading the budget left empty is marked as such in the rendered text. In both modes the body sections spend the budget first and back-matter sections share what the body, tables, and assets leave. Use it to survey what an article contains before requesting specific `sections`. Ignored when no budget is set, and identical for `source=unpaywall` bodies, which have no headings to preserve."Input schema / properties / pmcids / descriptionPrevious value: -"PMC IDs to fetch (e.g. [\"PMC9575052\"]). Combinable with `pmids` and `dois` — at most 10 distinct identifiers across the three. PMC IDs with no retrievable full text fall through to Europe PMC, then to Unpaywall on the DOI the chain resolves for them."New value: +"PMC IDs to fetch (e.g. [\"PMC9575052\"]). Combinable with `pmids` and `dois` — up to 50 distinct identifiers across the three; the first 10 are fetched per call, the rest returned in `overLimit`. PMC IDs with no retrievable full text fall through to Europe PMC, then to Unpaywall on the DOI the chain resolves for them."Input schema / properties / pmcids / maxItemsPrevious value: -10New value: +50Input schema / properties / pmids / descriptionPrevious value: -"PubMed IDs. Combinable with `pmcids` and `dois` — at most 10 distinct identifiers across the three. Articles in PMC are returned as structured JATS; articles not in PMC fall through to Europe PMC (when EPMC has a `fullTextXML`), then to Unpaywall when `UNPAYWALL_EMAIL` is set and a DOI is available."New value: +"PubMed IDs. Combinable with `pmcids` and `dois` — up to 50 distinct identifiers across the three; the first 10 are fetched per call, the rest returned in `overLimit`. Articles in PMC are returned as structured JATS; articles not in PMC fall through to Europe PMC (when EPMC has a `fullTextXML`), then to Unpaywall when `UNPAYWALL_EMAIL` is set and a DOI is available."Input schema / properties / pmids / maxItemsPrevious value: -10New value: +50Input schema / properties / sections / descriptionPrevious value: -"Filter to specific sections by title (e.g. [\"Introduction\", \"Methods\", \"Results\", \"Discussion\"]). A term matches a section or subsection title at any nesting depth, case-insensitively, as a substring — \"resul\" matches \"Results\". A section whose own title matches is returned whole; one kept only because a nested subsection matched keeps its heading as a breadcrumb, with its own text cleared and only the matching branch beneath it. Tables and assets narrow with the filter: one whose section did not survive, or that names no section, is dropped. Empty strings are skipped, so `[\"\"]` applies no filter; an element of only whitespace or invisible characters, such as a zero-width space, is rejected. Applies to `source=pmc` results only."New value: +"Filter to specific sections by title (e.g. [\"Introduction\", \"Methods\", \"Results\", \"Discussion\"]). A term matches a section or subsection title at any nesting depth, case-insensitively, as a substring — \"resul\" matches \"Results\". Back-matter sections match the same way: by their own titles, or by their kind when they carry neither a title nor a label — \"appendix\" matches a section titled \"Appendix A\", \"footnotes\" an untitled footnote group. A label is never matched, so an appendix labelled \"Appendix A\" under a title of its own matches only on that title. A section whose own title matches is returned whole; one kept only because a nested subsection matched keeps its heading as a breadcrumb, with its own text cleared and only the matching branch beneath it. Tables and assets narrow with the filter: one whose section did not survive, or that names no section, is dropped. Empty strings are skipped, so `[\"\"]` applies no filter; an element of only whitespace or invisible characters, such as a zero-width space, is rejected. Applies to `source=pmc` results only."Output schema / properties / articles / items / oneOfPrevious value: -[
- {
- "additionalProperties": false,
- "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
- "properties": {
- "abstract": {
- "description": "Abstract",
- "type": "string"
- },
- "affiliations": {
- "description": "Author affiliations",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "articleType": {
- "description": "Article type",
- "type": "string"
- },
- "assets": {
- "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from the body leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One figure or supplementary-material item, with its caption, pointer, and section",
- "properties": {
- "assetType": {
- "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
- "enum": [
- "figure",
- "supplementary-material"
- ],
- "type": "string"
- },
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "href": {
- "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
- "type": "string"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Display label as printed, e.g. `Fig. 1`",
- "type": "string"
- },
- "sectionTitle": {
- "description": "Title of the innermost section enclosing the asset, wherever that section sits — body, `<back>` matter, or an appendix all count. Absent for an asset inside no section at all, such as a `<floats-group>` deposit.",
- "type": "string"
- }
- },
- "required": [
- "assetType"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "authors": {
- "description": "Authors",
- "items": {
- "additionalProperties": false,
- "description": "Author entry",
- "properties": {
- "collectiveName": {
- "description": "Group name",
- "type": "string"
- },
- "givenNames": {
- "description": "Given names",
- "type": "string"
- },
- "lastName": {
- "description": "Last name",
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "doi": {
- "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
- "type": "string"
- },
- "epmcId": {
- "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
- "type": "string"
- },
- "epmcSource": {
- "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
- "type": "string"
- },
- "journal": {
- "additionalProperties": false,
- "description": "Journal information",
- "properties": {
- "elocationId": {
- "description": "Electronic article locator from JATS `<elocation-id>` — the publisher-assigned article number (e.g. \"e20542\"). Journals that assign article numbers deposit no `<fpage>`, so this is the only locator on roughly half of PMC records. Never a substitute for `pages`; JATS carries no type attribute, so there is no counterpart to the `elocationIdType` that `pubmed_fetch_articles` reports.",
- "type": "string"
- },
- "issn": {
- "description": "ISSN",
- "type": "string"
- },
- "issue": {
- "description": "Issue number",
- "type": "string"
- },
- "pages": {
- "description": "Page range",
- "type": "string"
- },
- "title": {
- "description": "Journal title",
- "type": "string"
- },
- "volume": {
- "description": "Volume number",
- "type": "string"
- }
- },
- "type": "object"
- },
- "keywords": {
- "description": "Keywords",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "pmcId": {
- "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
- "type": "string"
- },
- "pmcUrl": {
- "description": "PMC URL — derived from `pmcId` when present",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID",
- "type": "string"
- },
- "publicationDate": {
- "additionalProperties": false,
- "description": "Publication date",
- "properties": {
- "day": {
- "description": "Publication day",
- "type": "string"
- },
- "month": {
- "description": "Publication month",
- "type": "string"
- },
- "year": {
- "description": "Publication year",
- "type": "string"
- }
- },
- "type": "object"
- },
- "pubmedUrl": {
- "description": "PubMed URL",
- "type": "string"
- },
- "references": {
- "description": "Reference list",
- "items": {
- "additionalProperties": false,
- "description": "Reference entry",
- "properties": {
- "citation": {
- "description": "Citation text",
- "type": "string"
- },
- "id": {
- "description": "Reference ID",
- "type": "string"
- },
- "label": {
- "description": "Reference label",
- "type": "string"
- }
- },
- "required": [
- "citation"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "sections": {
- "description": "Article body sections",
- "items": {
- "additionalProperties": false,
- "description": "Article body section",
- "properties": {
- "label": {
- "description": "Section label",
- "type": "string"
- },
- "subsections": {
- "description": "Nested subsections",
- "items": {
- "additionalProperties": false,
- "description": "Article subsection",
- "properties": {
- "label": {
- "description": "Subsection label",
- "type": "string"
- },
- "text": {
- "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
- "type": "string"
- },
- "title": {
- "description": "Subsection heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "text": {
- "description": "Section body text",
- "type": "string"
- },
- "title": {
- "description": "Section heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "source": {
- "const": "pmc",
- "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
- "type": "string"
- },
- "tables": {
- "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One table from the article, with its cells, caption, and owning section",
- "properties": {
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "footnotes": {
- "description": "`<table-wrap-foot>` text, one line per footnote or paragraph, joined by `\\n`. A footnote marker deposited as a `<label>` leads its line, followed by a space (`* No patient …`).",
- "type": "string"
- },
- "headerRowCount": {
- "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
- "type": "number"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Table label as printed, e.g. `TABLE 1`",
- "type": "string"
- },
- "rows": {
- "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. A line break in a cell — a `<break/>`, a paragraph, or a list item in the source — is kept as `\\n`, so `1.08\\n2.44` is two values; superscripts and other inline markup are never spaced (`0.108a`). Empty when `unextractableReason` is set.",
- "items": {
- "description": "One row, as cell text by grid column",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "type": "array"
- },
- "sectionTitle": {
- "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
- "type": "string"
- },
- "unextractableReason": {
- "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
- "enum": [
- "cals-tgroup",
- "graphic-only",
- "no-rows"
- ],
- "type": "string"
- }
- },
- "required": [
- "headerRowCount",
- "rows"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "title": {
- "description": "Article title",
- "type": "string"
- },
- "viaSource": {
- "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
- "enum": [
- "pmc",
- "europepmc"
- ],
- "type": "string"
- }
- },
- "required": [
- "source",
- "viaSource",
- "sections"
- ],
- "type": "object"
- },
- {
- "additionalProperties": false,
- "description": "Best-effort full text from an open-access copy",
- "properties": {
- "content": {
- "description": "Full article text — Markdown or plain text per `contentFormat`",
- "type": "string"
- },
- "contentFormat": {
- "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
- "enum": [
- "html-markdown",
- "pdf-text"
- ],
- "type": "string"
- },
- "doi": {
- "description": "DOI used to locate the open-access copy",
- "type": "string"
- },
- "hostType": {
- "description": "`publisher` or `repository` — where the OA copy is hosted",
- "type": "string"
- },
- "journalName": {
- "description": "Journal or repository name from Unpaywall's record for the DOI (e.g. `medRxiv` for a medRxiv preprint). Absent when Unpaywall has none.",
- "type": "string"
- },
- "license": {
- "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
- "type": "string"
- },
- "pmcId": {
- "description": "PMC ID this article was requested under, in `PMC<digits>` form — present when a `pmcids` entry named it, absent when it was requested under a PMID or DOI. When several identifiers name one article, it is requested under the first to reach it: `pmcids`, then `pmids`, then `dois`. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID this article was requested under — present when it was requested under a `pmids` entry, absent when under a PMC ID or DOI (see `pmcId` for which identifier an article several of them name is requested under)",
- "type": "string"
- },
- "pubmedUrl": {
- "description": "PubMed URL — present when `pmid` is set",
- "type": "string"
- },
- "source": {
- "const": "unpaywall",
- "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
- "type": "string"
- },
- "sourceUrl": {
- "description": "URL the content was fetched from",
- "type": "string"
- },
- "title": {
- "description": "Article title, from the first source that carries one: Unpaywall's record for the DOI, then the Europe PMC record when the chain searched Europe PMC for this id, then — for `html-markdown` content only — the title detected on the page. Absent when none of them has a title.",
- "type": "string"
- },
- "totalPages": {
- "description": "Page count reported by the PDF extractor; absent for HTML",
- "type": "number"
- },
- "version": {
- "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
- "type": "string"
- },
- "viaSource": {
- "const": "unpaywall",
- "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
- "type": "string"
- },
- "wordCount": {
- "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
- "type": "number"
- },
- "year": {
- "description": "Publication year from Unpaywall's record for the DOI. Absent when Unpaywall has none.",
- "type": "number"
- }
- },
- "required": [
- "source",
- "viaSource",
- "contentFormat",
- "doi",
- "sourceUrl",
- "content"
- ],
- "type": "object"
- }
-]New value: +[
+ {
+ "additionalProperties": false,
+ "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
+ "properties": {
+ "abstract": {
+ "description": "Abstract",
+ "type": "string"
+ },
+ "affiliations": {
+ "description": "Author affiliations",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "articleType": {
+ "description": "Article type",
+ "type": "string"
+ },
+ "assets": {
+ "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from a section, body or back matter, leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One figure or supplementary-material item, with its caption, pointer, and section",
+ "properties": {
+ "assetType": {
+ "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
+ "enum": [
+ "figure",
+ "supplementary-material"
+ ],
+ "type": "string"
+ },
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "href": {
+ "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
+ "type": "string"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Display label as printed, e.g. `Fig. 1`",
+ "type": "string"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost titled section enclosing the asset — a body section or a back-matter one such as an appendix — as that section is titled in `sections`, or, for a heading nested deeper than `sections` carries, as its heading line inside the text of the section that contains it. Absent for an asset inside no titled section, such as a `<floats-group>` deposit.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "assetType"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "authors": {
+ "description": "Authors",
+ "items": {
+ "additionalProperties": false,
+ "description": "Author entry",
+ "properties": {
+ "collectiveName": {
+ "description": "Group name",
+ "type": "string"
+ },
+ "givenNames": {
+ "description": "Given names",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Last name",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "doi": {
+ "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
+ "type": "string"
+ },
+ "epmcId": {
+ "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
+ "type": "string"
+ },
+ "epmcSource": {
+ "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
+ "type": "string"
+ },
+ "journal": {
+ "additionalProperties": false,
+ "description": "Journal information",
+ "properties": {
+ "elocationId": {
+ "description": "Electronic article locator from JATS `<elocation-id>` — the publisher-assigned article number (e.g. \"e20542\"). Journals that assign article numbers deposit no `<fpage>`, so this is the only locator on roughly half of PMC records. Never a substitute for `pages`; JATS carries no type attribute, so there is no counterpart to the `elocationIdType` that `pubmed_fetch_articles` reports.",
+ "type": "string"
+ },
+ "issn": {
+ "description": "ISSN",
+ "type": "string"
+ },
+ "issue": {
+ "description": "Issue number",
+ "type": "string"
+ },
+ "pages": {
+ "description": "Page range",
+ "type": "string"
+ },
+ "title": {
+ "description": "Journal title",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "keywords": {
+ "description": "Keywords",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "pmcId": {
+ "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
+ "type": "string"
+ },
+ "pmcUrl": {
+ "description": "PMC URL — derived from `pmcId` when present",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID",
+ "type": "string"
+ },
+ "publicationDate": {
+ "additionalProperties": false,
+ "description": "Publication date",
+ "properties": {
+ "day": {
+ "description": "Publication day",
+ "type": "string"
+ },
+ "month": {
+ "description": "Publication month",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL",
+ "type": "string"
+ },
+ "references": {
+ "description": "Reference list",
+ "items": {
+ "additionalProperties": false,
+ "description": "Reference entry",
+ "properties": {
+ "citation": {
+ "description": "Citation text",
+ "type": "string"
+ },
+ "id": {
+ "description": "Reference ID",
+ "type": "string"
+ },
+ "label": {
+ "description": "Reference label",
+ "type": "string"
+ }
+ },
+ "required": [
+ "citation"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "sections": {
+ "description": "Article sections in source order: the body, then the back matter — acknowledgments, notes and declarations, footnotes, glossary, appendices. A back-matter element with no heading of its own is titled by its kind, such as `Footnotes` or `Appendix`.",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article section, from the body or from the back matter after it",
+ "properties": {
+ "label": {
+ "description": "Section label",
+ "type": "string"
+ },
+ "subsections": {
+ "description": "Nested subsections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article subsection",
+ "properties": {
+ "label": {
+ "description": "Subsection label",
+ "type": "string"
+ },
+ "text": {
+ "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
+ "type": "string"
+ },
+ "title": {
+ "description": "Subsection heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "text": {
+ "description": "Section body text",
+ "type": "string"
+ },
+ "title": {
+ "description": "Section heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "source": {
+ "const": "pmc",
+ "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
+ "type": "string"
+ },
+ "tables": {
+ "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One table from the article, with its cells, caption, and owning section",
+ "properties": {
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "footnotes": {
+ "description": "`<table-wrap-foot>` text, one line per footnote or paragraph, joined by `\\n`. A footnote marker deposited as a `<label>` leads its line, followed by a space (`* No patient …`).",
+ "type": "string"
+ },
+ "headerRowCount": {
+ "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
+ "type": "number"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Table label as printed, e.g. `TABLE 1`",
+ "type": "string"
+ },
+ "rows": {
+ "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. A line break in a cell — a `<break/>`, a paragraph, or a list item in the source — is kept as `\\n`, so `1.08\\n2.44` is two values; superscripts and other inline markup are never spaced (`0.108a`). Empty when `unextractableReason` is set.",
+ "items": {
+ "description": "One row, as cell text by grid column",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "type": "array"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost titled section enclosing the table — a body section or a back-matter one such as an appendix — as that section is titled in `sections`, or, for a heading nested deeper than `sections` carries, as its heading line inside the text of the section that contains it. A `sections` filter keeps the table with that section. In back matter the section name is the only positional cue there is. Absent for a table inside no titled section, such as a `<floats-group>` deposit.",
+ "type": "string"
+ },
+ "unextractableReason": {
+ "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
+ "enum": [
+ "cals-tgroup",
+ "graphic-only",
+ "no-rows"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "headerRowCount",
+ "rows"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "title": {
+ "description": "Article title",
+ "type": "string"
+ },
+ "viaSource": {
+ "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
+ "enum": [
+ "pmc",
+ "europepmc"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "sections"
+ ],
+ "type": "object"
+ },
+ {
+ "additionalProperties": false,
+ "description": "Best-effort full text from an open-access copy",
+ "properties": {
+ "content": {
+ "description": "Full article text — Markdown or plain text per `contentFormat`",
+ "type": "string"
+ },
+ "contentFormat": {
+ "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
+ "enum": [
+ "html-markdown",
+ "pdf-text"
+ ],
+ "type": "string"
+ },
+ "doi": {
+ "description": "DOI used to locate the open-access copy",
+ "type": "string"
+ },
+ "hostType": {
+ "description": "`publisher` or `repository` — where the OA copy is hosted",
+ "type": "string"
+ },
+ "journalName": {
+ "description": "Journal or repository name from Unpaywall's record for the DOI (e.g. `medRxiv` for a medRxiv preprint). Absent when Unpaywall has none.",
+ "type": "string"
+ },
+ "license": {
+ "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
+ "type": "string"
+ },
+ "pmcId": {
+ "description": "PMC ID this article was requested under, in `PMC<digits>` form — present when a `pmcids` entry named it, absent when it was requested under a PMID or DOI. When several identifiers name one article, it is requested under the first to reach it: `pmcids`, then `pmids`, then `dois`. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID this article was requested under — present when it was requested under a `pmids` entry, absent when under a PMC ID or DOI (see `pmcId` for which identifier an article several of them name is requested under)",
+ "type": "string"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL — present when `pmid` is set",
+ "type": "string"
+ },
+ "source": {
+ "const": "unpaywall",
+ "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
+ "type": "string"
+ },
+ "sourceUrl": {
+ "description": "URL the content was fetched from",
+ "type": "string"
+ },
+ "title": {
+ "description": "Article title, from the first source that carries one: Unpaywall's record for the DOI, then the Europe PMC record when the chain searched Europe PMC for this id, then — for `html-markdown` content only — the title detected on the page. Absent when none of them has a title.",
+ "type": "string"
+ },
+ "totalPages": {
+ "description": "Page count reported by the PDF extractor; absent for HTML",
+ "type": "number"
+ },
+ "version": {
+ "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
+ "type": "string"
+ },
+ "viaSource": {
+ "const": "unpaywall",
+ "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
+ "type": "string"
+ },
+ "wordCount": {
+ "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
+ "type": "number"
+ },
+ "year": {
+ "description": "Publication year from Unpaywall's record for the DOI. Absent when Unpaywall has none.",
+ "type": "number"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "contentFormat",
+ "doi",
+ "sourceUrl",
+ "content"
+ ],
+ "type": "object"
+ }
+]Output schema / properties / notice / descriptionPrevious value: -"Optional guidance for a partial or empty body. A `sections`-filter miss names the requested terms and affected article id(s) and suggests retrying without `sections` or using broader headings. A metadata-only record names the id(s) the chain could retrieve as front matter only and points at `pubmed_fetch_articles` for the abstract. A table returned with no cell values names the affected table(s), the article each came from, and why the cells cannot be recovered. A budgeted response names the characters returned versus carried and points at `truncation`. A response-wide budget that deferred articles names the ids to re-request. Absent when none of those applies."New value: +"Optional guidance for a partial or empty body. A `sections`-filter miss names the requested terms and affected article id(s) and suggests retrying without `sections` or using broader headings. A metadata-only record names the id(s) the chain could retrieve as front matter only and points at `pubmed_fetch_articles` for the abstract. A table returned with no cell values names the affected table(s), the article each came from, and why the cells cannot be recovered. A budgeted response names the characters returned versus carried and points at `truncation`. A response-wide budget that deferred articles names the ids to re-request. Identifiers past the per-call limit are named with the field to resend each under. Absent when none of those applies."Output schema / properties / overLimitAdded value: +{
+ "additionalProperties": false,
+ "description": "Identifiers the call named past the per-call fetch limit, returned unfetched for a follow-up call. Present only when the call named more than `limit` distinct identifiers. Separate from `deferred`, which lists articles that were fetched but withheld by `maxResponseCharacters`.",
+ "properties": {
+ "dois": {
+ "description": "The over-limit ids sent as DOIs, in routing order — re-submit them as `dois`. Present only when the over-limit ids came from more than one field (so `idType` is absent) and one of them was a DOI.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "idType": {
+ "description": "The input field every over-limit id was sent in — re-submit them as `pmids`, `pmcids`, or `dois` respectively. Absent when the over-limit ids came from more than one field; `pmcids` / `pmids` / `dois` then group them.",
+ "enum": [
+ "pmid",
+ "pmcid",
+ "doi"
+ ],
+ "type": "string"
+ },
+ "ids": {
+ "description": "Identifiers past the per-call limit, none of them fetched, in routing order — each listed once, under the first spelling sent (PMC IDs in `PMC<digits>` form). Re-call `pubmed_fetch_fulltext` with these under the `idType` field — or, when `idType` is absent, with the `pmcids` / `pmids` / `dois` lists below — and the same other inputs, at most `limit` per call. Never contains an id from `unavailable` or `deferred`.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "limit": {
+ "description": "Distinct identifiers one call fetches. The first this many, in routing order — `pmcids`, then `pmids`, then `dois`, request order within each — were fetched; the ids below were not.",
+ "type": "number"
+ },
+ "pmcids": {
+ "description": "The over-limit ids sent as PMC IDs, in routing order — re-submit them as `pmcids`. Present only when the over-limit ids came from more than one field (so `idType` is absent) and one of them was a PMC ID.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "pmids": {
+ "description": "The over-limit ids sent as PMIDs, in routing order — re-submit them as `pmids`. Present only when the over-limit ids came from more than one field (so `idType` is absent) and one of them was a PMID.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ }
+ },
+ "required": [
+ "limit",
+ "ids"
+ ],
+ "type": "object"
+}Output schema / properties / truncated / descriptionPrevious value: -"True when a character budget shortened at least one returned body, or withheld a whole article. Absent when every resolved article is present with its full post-filter body. The per-article body accounting is in `truncation`; the withheld ids are in `deferred`."New value: +"True when a character budget shortened at least one returned body or withheld a whole article, or when the call named more distinct identifiers than one call fetches. Absent when every requested identifier was fetched and every resolved article is present with its full post-filter body. The per-article body accounting is in `truncation`; the withheld ids are in `deferred`; the unfetched ids are in `overLimit`."Output schema / properties / truncation / properties / articles / items / properties / omittedAssets / descriptionPrevious value: -"Figures and supplementary items this article dropped whole because the budget left no room once sections and tables were served. An asset is never returned with a truncated caption, so it is either returned complete or counted here. Absent when none were dropped."New value: +"Figures and supplementary items this article dropped whole because the budget left no room once body sections and tables were served. An asset is never returned with a truncated caption, so it is either returned complete or counted here. Absent when none were dropped."Output schema / properties / truncation / properties / articles / items / properties / sections / items / descriptionPrevious value: -"Character accounting for one body section of a budgeted article"New value: +"Character accounting for one section of a budgeted article"Output schema / properties / truncation / properties / articles / items / properties / source / descriptionPrevious value: -"Which output shape was budgeted: `pmc` budgets body sections and subsections, `unpaywall` budgets the single `content` body"New value: +"Which output shape was budgeted: `pmc` budgets sections and subsections, `unpaywall` budgets the single `content` body"Output schema / properties / truncation / properties / omittedSections / descriptionPrevious value: -"Body sections and subsections dropped entirely because an article budget was exhausted before reaching them. A dropped section counts once, together with its subsections. Always 0 in `outline` mode, which keeps every heading."New value: +"Sections and subsections, back matter included, dropped entirely because an article budget was exhausted before reaching them. Back matter is reached last, after tables and assets. A dropped section counts once, together with its subsections. Always 0 in `outline` mode, which keeps every heading."Output schema / properties / unavailable / descriptionPrevious value: -"Per-identifier explanations for any requested PMIDs, PMCIDs, or DOIs with no returnable full text. `idType` names the field each id was sent in. Distinct from `deferred`: nothing here is retrievable by re-calling, and an id never appears in both."New value: +"Per-identifier explanations for any requested PMIDs, PMCIDs, or DOIs with no returnable full text. `idType` names the field each id was sent in. Distinct from `deferred`: nothing here is retrievable by re-calling, and an id never appears in both. Ids past the per-call limit are listed in `overLimit`, never here."pubmed_format_citations1 field changedOutput schema / properties / citations / items / properties / noticesAdded value: +{
+ "description": "Retraction, erratum, and expression-of-concern notices NCBI links to this article, in NCBI's order. Vancouver notes each `RetractionIn` and `ErratumIn` after the reference and APA each `RetractionIn`; the other types, and MLA, BibTeX, and RIS, carry none, so check this before citing. Absent when NCBI links none.",
+ "items": {
+ "additionalProperties": false,
+ "description": "A linked notice that qualifies the cited article",
+ "properties": {
+ "note": {
+ "description": "NCBI's note on the link, e.g. the correction an erratum makes. Absent when NCBI gives none.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PMID of the notice — pass it to `pubmed_fetch_articles` to read it. Absent when the notice has no PMID, as with many errata.",
+ "type": "string"
+ },
+ "refSource": {
+ "description": "Citation of the notice as NCBI writes it (e.g. \"Lancet. 2010 Feb 6;375(9713):445. doi: 10.1016/S0140-6736(10)60175-4.\").",
+ "type": "string"
+ },
+ "refType": {
+ "description": "NCBI's `RefType` for the link: RetractionIn, RetractedandRepublishedIn, ExpressionOfConcernIn, ErratumIn, or CorrectedandRepublishedIn.",
+ "enum": [
+ "RetractionIn",
+ "RetractedandRepublishedIn",
+ "ExpressionOfConcernIn",
+ "ErratumIn",
+ "CorrectedandRepublishedIn"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "refType",
+ "refSource"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+}pubmed_europepmc_fetch6 fields changedInput schema / properties / maxResponseCharactersAdded value: +{
+ "description": "Opt-in ceiling for the whole response, in characters. Each record is measured as the JSON record it is returned as — title, authors, journal, abstract, identifiers, every field it carries. Records are kept in the order Europe PMC returned them until the next one would cross the ceiling; that record and the rest are deferred whole (never partially populated) and listed in `deferred.records`. Response envelope fields — `notFound`, `deferred` itself — are not counted. Omit to return every resolved record.",
+ "maximum": 1000000,
+ "minimum": 1,
+ "type": "integer"
+}Output schema / properties / deferredAdded value: +{
+ "additionalProperties": false,
+ "description": "Continuation state for records the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one record.",
+ "properties": {
+ "deferredCount": {
+ "description": "Records that resolved but were withheld to stay under the ceiling",
+ "type": "number"
+ },
+ "maxResponseCharacters": {
+ "description": "The `maxResponseCharacters` ceiling this response was budgeted against",
+ "type": "number"
+ },
+ "nextDeferredCharacters": {
+ "description": "Serialized size of the next deferred record — the first entry in `records`, where the response stopped. Raise `maxResponseCharacters` to at least this to make progress; a smaller record further down `records` cannot be reached until this one fits.",
+ "type": "number"
+ },
+ "records": {
+ "description": "The deferred records, in response order, each as the resolved record's own `source` + `epmcId` — a `PMC` request answered by its `MED` record is listed as that `MED` pair. Pass them back as `records` to retrieve them. Never contains a pair from `notFound`.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One deferred record, addressed by its own `source` + `epmcId`",
+ "properties": {
+ "epmcId": {
+ "description": "Europe PMC's internal record id",
+ "type": "string"
+ },
+ "source": {
+ "description": "Europe PMC source the record was resolved from",
+ "enum": [
+ "MED",
+ "PMC",
+ "PPR",
+ "PAT",
+ "AGR"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "source",
+ "epmcId"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "returnedCharacters": {
+ "description": "Serialized characters the returned records account for",
+ "type": "number"
+ }
+ },
+ "required": [
+ "maxResponseCharacters",
+ "returnedCharacters",
+ "deferredCount",
+ "records",
+ "nextDeferredCharacters"
+ ],
+ "type": "object"
+}Output schema / properties / notFound / descriptionPrevious value: -"Requested `source` + `epmcId` pairs Europe PMC returned no record for"New value: +"Requested `source` + `epmcId` pairs Europe PMC returned no record for. Reported in full regardless of where a `maxResponseCharacters` cut lands — these are misses, not deferrals."Output schema / properties / notice / descriptionPrevious value: -"Guidance when one or more requested records could not be resolved. Absent when every record came back."New value: +"Guidance when one or more requested records could not be resolved, or when `maxResponseCharacters` deferred records — naming how to retrieve them. Absent when every requested record came back."Output schema / properties / records / descriptionPrevious value: -"Resolved records, in the order Europe PMC returned them"New value: +"Resolved records, in the order Europe PMC returned them. Under a `maxResponseCharacters` budget, only the leading records that fit; `deferred.records` lists the rest."Output schema / properties / truncatedAdded value: +{
+ "description": "True when `maxResponseCharacters` withheld at least one resolved record. Absent when the response carries every record that resolved. The continuation state is in `deferred`.",
+ "type": "boolean"
+}pubmed_fetch_articles2 fields changedOutput schema / properties / articles / items / properties / articleDates / descriptionPrevious value: -"Article dates"New value: +"Dates of the record itself, each named by `dateType`. On a journal article, PubMed's `ArticleDate` entries (`Electronic` — the electronic publication date). On a Bookshelf record, its own `ContributionDate` (when the chapter was contributed) and `DateRevised` (when it was last updated), distinct from the containing book's dates in `book`; `pubmed_format_citations` cites a chapter by `DateRevised` when present, otherwise `ContributionDate`. Absent when NCBI supplies none."Output schema / properties / articles / items / properties / grantList / items / properties / acronym / descriptionPrevious value: -"Grant acronym"New value: +"Acronym of the funding institute or agency from `Grant/Acronym` (e.g. \"EY\" for the National Eye Institute) — it names the funder, never the grant, so it is no substitute for `grantId`."pubmed_fetch_fulltext15 fields changedInput schema / properties / dois / descriptionPrevious value: -"DOIs to resolve (e.g. [\"10.21203/rs.3.rs-9010375/v1\"]), one per element. Provide exactly one of `pmcids`, `pmids`, or `dois`. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled."New value: +"DOIs to resolve (e.g. [\"10.21203/rs.3.rs-9010375/v1\"]), one per element. Combinable with `pmcids` and `pmids` — at most 10 distinct identifiers across the three. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled."Input schema / properties / pmcids / descriptionPrevious value: -"PMC IDs to fetch (e.g. [\"PMC9575052\"]). Provide exactly one of `pmcids`, `pmids`, or `dois`. PMC IDs with no retrievable full text fall through to Europe PMC, then to Unpaywall on the DOI the chain resolves for them."New value: +"PMC IDs to fetch (e.g. [\"PMC9575052\"]). Combinable with `pmids` and `dois` — at most 10 distinct identifiers across the three. PMC IDs with no retrievable full text fall through to Europe PMC, then to Unpaywall on the DOI the chain resolves for them."Input schema / properties / pmids / descriptionPrevious value: -"PubMed IDs. Provide exactly one of `pmcids`, `pmids`, or `dois`. Articles in PMC are returned as structured JATS; articles not in PMC fall through to Europe PMC (when EPMC has a `fullTextXML`), then to Unpaywall when `UNPAYWALL_EMAIL` is set and a DOI is available."New value: +"PubMed IDs. Combinable with `pmcids` and `dois` — at most 10 distinct identifiers across the three. Articles in PMC are returned as structured JATS; articles not in PMC fall through to Europe PMC (when EPMC has a `fullTextXML`), then to Unpaywall when `UNPAYWALL_EMAIL` is set and a DOI is available."Input schema / properties / sections / descriptionPrevious value: -"Filter to specific sections by title (e.g. [\"Introduction\", \"Methods\", \"Results\", \"Discussion\"]). A term matches a section or subsection title at any nesting depth, case-insensitively, as a substring — \"resul\" matches \"Results\". A section whose own title matches is returned whole; one kept only because a nested subsection matched keeps its heading as a breadcrumb, with its own text cleared and only the matching branch beneath it. Tables and assets narrow with the filter: one whose section did not survive, or that names no section, is dropped. Applies to `source=pmc` results only."New value: +"Filter to specific sections by title (e.g. [\"Introduction\", \"Methods\", \"Results\", \"Discussion\"]). A term matches a section or subsection title at any nesting depth, case-insensitively, as a substring — \"resul\" matches \"Results\". A section whose own title matches is returned whole; one kept only because a nested subsection matched keeps its heading as a breadcrumb, with its own text cleared and only the matching branch beneath it. Tables and assets narrow with the filter: one whose section did not survive, or that names no section, is dropped. Empty strings are skipped, so `[\"\"]` applies no filter; an element of only whitespace or invisible characters, such as a zero-width space, is rejected. Applies to `source=pmc` results only."Output schema / properties / articles / items / oneOfPrevious value: -[
- {
- "additionalProperties": false,
- "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
- "properties": {
- "abstract": {
- "description": "Abstract",
- "type": "string"
- },
- "affiliations": {
- "description": "Author affiliations",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "articleType": {
- "description": "Article type",
- "type": "string"
- },
- "assets": {
- "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from the body leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One figure or supplementary-material item, with its caption, pointer, and section",
- "properties": {
- "assetType": {
- "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
- "enum": [
- "figure",
- "supplementary-material"
- ],
- "type": "string"
- },
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "href": {
- "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
- "type": "string"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Display label as printed, e.g. `Fig. 1`",
- "type": "string"
- },
- "sectionTitle": {
- "description": "Title of the innermost section enclosing the asset, wherever that section sits — body, `<back>` matter, or an appendix all count. Absent for an asset inside no section at all, such as a `<floats-group>` deposit.",
- "type": "string"
- }
- },
- "required": [
- "assetType"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "authors": {
- "description": "Authors",
- "items": {
- "additionalProperties": false,
- "description": "Author entry",
- "properties": {
- "collectiveName": {
- "description": "Group name",
- "type": "string"
- },
- "givenNames": {
- "description": "Given names",
- "type": "string"
- },
- "lastName": {
- "description": "Last name",
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "doi": {
- "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
- "type": "string"
- },
- "epmcId": {
- "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
- "type": "string"
- },
- "epmcSource": {
- "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
- "type": "string"
- },
- "journal": {
- "additionalProperties": false,
- "description": "Journal information",
- "properties": {
- "elocationId": {
- "description": "Electronic article locator from JATS `<elocation-id>` — the publisher-assigned article number (e.g. \"e20542\"). Journals that assign article numbers deposit no `<fpage>`, so this is the only locator on roughly half of PMC records. Never a substitute for `pages`; JATS carries no type attribute, so there is no counterpart to the `elocationIdType` that `pubmed_fetch_articles` reports.",
- "type": "string"
- },
- "issn": {
- "description": "ISSN",
- "type": "string"
- },
- "issue": {
- "description": "Issue number",
- "type": "string"
- },
- "pages": {
- "description": "Page range",
- "type": "string"
- },
- "title": {
- "description": "Journal title",
- "type": "string"
- },
- "volume": {
- "description": "Volume number",
- "type": "string"
- }
- },
- "type": "object"
- },
- "keywords": {
- "description": "Keywords",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "pmcId": {
- "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
- "type": "string"
- },
- "pmcUrl": {
- "description": "PMC URL — derived from `pmcId` when present",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID",
- "type": "string"
- },
- "publicationDate": {
- "additionalProperties": false,
- "description": "Publication date",
- "properties": {
- "day": {
- "description": "Publication day",
- "type": "string"
- },
- "month": {
- "description": "Publication month",
- "type": "string"
- },
- "year": {
- "description": "Publication year",
- "type": "string"
- }
- },
- "type": "object"
- },
- "pubmedUrl": {
- "description": "PubMed URL",
- "type": "string"
- },
- "references": {
- "description": "Reference list",
- "items": {
- "additionalProperties": false,
- "description": "Reference entry",
- "properties": {
- "citation": {
- "description": "Citation text",
- "type": "string"
- },
- "id": {
- "description": "Reference ID",
- "type": "string"
- },
- "label": {
- "description": "Reference label",
- "type": "string"
- }
- },
- "required": [
- "citation"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "sections": {
- "description": "Article body sections",
- "items": {
- "additionalProperties": false,
- "description": "Article body section",
- "properties": {
- "label": {
- "description": "Section label",
- "type": "string"
- },
- "subsections": {
- "description": "Nested subsections",
- "items": {
- "additionalProperties": false,
- "description": "Article subsection",
- "properties": {
- "label": {
- "description": "Subsection label",
- "type": "string"
- },
- "text": {
- "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
- "type": "string"
- },
- "title": {
- "description": "Subsection heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "text": {
- "description": "Section body text",
- "type": "string"
- },
- "title": {
- "description": "Section heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "source": {
- "const": "pmc",
- "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
- "type": "string"
- },
- "tables": {
- "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One table from the article, with its cells, caption, and owning section",
- "properties": {
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "footnotes": {
- "description": "`<table-wrap-foot>` text, flattened to one string",
- "type": "string"
- },
- "headerRowCount": {
- "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
- "type": "number"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Table label as printed, e.g. `TABLE 1`",
- "type": "string"
- },
- "rows": {
- "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. Empty when `unextractableReason` is set.",
- "items": {
- "description": "One row, as cell text by grid column",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "type": "array"
- },
- "sectionTitle": {
- "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
- "type": "string"
- },
- "unextractableReason": {
- "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
- "enum": [
- "cals-tgroup",
- "graphic-only",
- "no-rows"
- ],
- "type": "string"
- }
- },
- "required": [
- "headerRowCount",
- "rows"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "title": {
- "description": "Article title",
- "type": "string"
- },
- "viaSource": {
- "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
- "enum": [
- "pmc",
- "europepmc"
- ],
- "type": "string"
- }
- },
- "required": [
- "source",
- "viaSource",
- "sections"
- ],
- "type": "object"
- },
- {
- "additionalProperties": false,
- "description": "Best-effort full text from an open-access copy",
- "properties": {
- "content": {
- "description": "Full article text — Markdown or plain text per `contentFormat`",
- "type": "string"
- },
- "contentFormat": {
- "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
- "enum": [
- "html-markdown",
- "pdf-text"
- ],
- "type": "string"
- },
- "doi": {
- "description": "DOI used to locate the open-access copy",
- "type": "string"
- },
- "hostType": {
- "description": "`publisher` or `repository` — where the OA copy is hosted",
- "type": "string"
- },
- "journalName": {
- "description": "Journal or repository name from Unpaywall's record for the DOI (e.g. `medRxiv` for a medRxiv preprint). Absent when Unpaywall has none.",
- "type": "string"
- },
- "license": {
- "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
- "type": "string"
- },
- "pmcId": {
- "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
- "type": "string"
- },
- "pubmedUrl": {
- "description": "PubMed URL — present when `pmid` is set",
- "type": "string"
- },
- "source": {
- "const": "unpaywall",
- "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
- "type": "string"
- },
- "sourceUrl": {
- "description": "URL the content was fetched from",
- "type": "string"
- },
- "title": {
- "description": "Article title, from the first source that carries one: Unpaywall's record for the DOI, then the Europe PMC record when the chain searched Europe PMC for this id, then — for `html-markdown` content only — the title detected on the page. Absent when none of them has a title.",
- "type": "string"
- },
- "totalPages": {
- "description": "Page count reported by the PDF extractor; absent for HTML",
- "type": "number"
- },
- "version": {
- "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
- "type": "string"
- },
- "viaSource": {
- "const": "unpaywall",
- "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
- "type": "string"
- },
- "wordCount": {
- "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
- "type": "number"
- },
- "year": {
- "description": "Publication year from Unpaywall's record for the DOI. Absent when Unpaywall has none.",
- "type": "number"
- }
- },
- "required": [
- "source",
- "viaSource",
- "contentFormat",
- "doi",
- "sourceUrl",
- "content"
- ],
- "type": "object"
- }
-]New value: +[
+ {
+ "additionalProperties": false,
+ "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
+ "properties": {
+ "abstract": {
+ "description": "Abstract",
+ "type": "string"
+ },
+ "affiliations": {
+ "description": "Author affiliations",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "articleType": {
+ "description": "Article type",
+ "type": "string"
+ },
+ "assets": {
+ "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from the body leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One figure or supplementary-material item, with its caption, pointer, and section",
+ "properties": {
+ "assetType": {
+ "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
+ "enum": [
+ "figure",
+ "supplementary-material"
+ ],
+ "type": "string"
+ },
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "href": {
+ "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
+ "type": "string"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Display label as printed, e.g. `Fig. 1`",
+ "type": "string"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost section enclosing the asset, wherever that section sits — body, `<back>` matter, or an appendix all count. Absent for an asset inside no section at all, such as a `<floats-group>` deposit.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "assetType"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "authors": {
+ "description": "Authors",
+ "items": {
+ "additionalProperties": false,
+ "description": "Author entry",
+ "properties": {
+ "collectiveName": {
+ "description": "Group name",
+ "type": "string"
+ },
+ "givenNames": {
+ "description": "Given names",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Last name",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "doi": {
+ "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
+ "type": "string"
+ },
+ "epmcId": {
+ "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
+ "type": "string"
+ },
+ "epmcSource": {
+ "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
+ "type": "string"
+ },
+ "journal": {
+ "additionalProperties": false,
+ "description": "Journal information",
+ "properties": {
+ "elocationId": {
+ "description": "Electronic article locator from JATS `<elocation-id>` — the publisher-assigned article number (e.g. \"e20542\"). Journals that assign article numbers deposit no `<fpage>`, so this is the only locator on roughly half of PMC records. Never a substitute for `pages`; JATS carries no type attribute, so there is no counterpart to the `elocationIdType` that `pubmed_fetch_articles` reports.",
+ "type": "string"
+ },
+ "issn": {
+ "description": "ISSN",
+ "type": "string"
+ },
+ "issue": {
+ "description": "Issue number",
+ "type": "string"
+ },
+ "pages": {
+ "description": "Page range",
+ "type": "string"
+ },
+ "title": {
+ "description": "Journal title",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "keywords": {
+ "description": "Keywords",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "pmcId": {
+ "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
+ "type": "string"
+ },
+ "pmcUrl": {
+ "description": "PMC URL — derived from `pmcId` when present",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID",
+ "type": "string"
+ },
+ "publicationDate": {
+ "additionalProperties": false,
+ "description": "Publication date",
+ "properties": {
+ "day": {
+ "description": "Publication day",
+ "type": "string"
+ },
+ "month": {
+ "description": "Publication month",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL",
+ "type": "string"
+ },
+ "references": {
+ "description": "Reference list",
+ "items": {
+ "additionalProperties": false,
+ "description": "Reference entry",
+ "properties": {
+ "citation": {
+ "description": "Citation text",
+ "type": "string"
+ },
+ "id": {
+ "description": "Reference ID",
+ "type": "string"
+ },
+ "label": {
+ "description": "Reference label",
+ "type": "string"
+ }
+ },
+ "required": [
+ "citation"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "sections": {
+ "description": "Article body sections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article body section",
+ "properties": {
+ "label": {
+ "description": "Section label",
+ "type": "string"
+ },
+ "subsections": {
+ "description": "Nested subsections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article subsection",
+ "properties": {
+ "label": {
+ "description": "Subsection label",
+ "type": "string"
+ },
+ "text": {
+ "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
+ "type": "string"
+ },
+ "title": {
+ "description": "Subsection heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "text": {
+ "description": "Section body text",
+ "type": "string"
+ },
+ "title": {
+ "description": "Section heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "source": {
+ "const": "pmc",
+ "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
+ "type": "string"
+ },
+ "tables": {
+ "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One table from the article, with its cells, caption, and owning section",
+ "properties": {
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "footnotes": {
+ "description": "`<table-wrap-foot>` text, one line per footnote or paragraph, joined by `\\n`. A footnote marker deposited as a `<label>` leads its line, followed by a space (`* No patient …`).",
+ "type": "string"
+ },
+ "headerRowCount": {
+ "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
+ "type": "number"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Table label as printed, e.g. `TABLE 1`",
+ "type": "string"
+ },
+ "rows": {
+ "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. A line break in a cell — a `<break/>`, a paragraph, or a list item in the source — is kept as `\\n`, so `1.08\\n2.44` is two values; superscripts and other inline markup are never spaced (`0.108a`). Empty when `unextractableReason` is set.",
+ "items": {
+ "description": "One row, as cell text by grid column",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "type": "array"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
+ "type": "string"
+ },
+ "unextractableReason": {
+ "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
+ "enum": [
+ "cals-tgroup",
+ "graphic-only",
+ "no-rows"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "headerRowCount",
+ "rows"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "title": {
+ "description": "Article title",
+ "type": "string"
+ },
+ "viaSource": {
+ "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
+ "enum": [
+ "pmc",
+ "europepmc"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "sections"
+ ],
+ "type": "object"
+ },
+ {
+ "additionalProperties": false,
+ "description": "Best-effort full text from an open-access copy",
+ "properties": {
+ "content": {
+ "description": "Full article text — Markdown or plain text per `contentFormat`",
+ "type": "string"
+ },
+ "contentFormat": {
+ "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
+ "enum": [
+ "html-markdown",
+ "pdf-text"
+ ],
+ "type": "string"
+ },
+ "doi": {
+ "description": "DOI used to locate the open-access copy",
+ "type": "string"
+ },
+ "hostType": {
+ "description": "`publisher` or `repository` — where the OA copy is hosted",
+ "type": "string"
+ },
+ "journalName": {
+ "description": "Journal or repository name from Unpaywall's record for the DOI (e.g. `medRxiv` for a medRxiv preprint). Absent when Unpaywall has none.",
+ "type": "string"
+ },
+ "license": {
+ "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
+ "type": "string"
+ },
+ "pmcId": {
+ "description": "PMC ID this article was requested under, in `PMC<digits>` form — present when a `pmcids` entry named it, absent when it was requested under a PMID or DOI. When several identifiers name one article, it is requested under the first to reach it: `pmcids`, then `pmids`, then `dois`. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID this article was requested under — present when it was requested under a `pmids` entry, absent when under a PMC ID or DOI (see `pmcId` for which identifier an article several of them name is requested under)",
+ "type": "string"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL — present when `pmid` is set",
+ "type": "string"
+ },
+ "source": {
+ "const": "unpaywall",
+ "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
+ "type": "string"
+ },
+ "sourceUrl": {
+ "description": "URL the content was fetched from",
+ "type": "string"
+ },
+ "title": {
+ "description": "Article title, from the first source that carries one: Unpaywall's record for the DOI, then the Europe PMC record when the chain searched Europe PMC for this id, then — for `html-markdown` content only — the title detected on the page. Absent when none of them has a title.",
+ "type": "string"
+ },
+ "totalPages": {
+ "description": "Page count reported by the PDF extractor; absent for HTML",
+ "type": "number"
+ },
+ "version": {
+ "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
+ "type": "string"
+ },
+ "viaSource": {
+ "const": "unpaywall",
+ "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
+ "type": "string"
+ },
+ "wordCount": {
+ "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
+ "type": "number"
+ },
+ "year": {
+ "description": "Publication year from Unpaywall's record for the DOI. Absent when Unpaywall has none.",
+ "type": "number"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "contentFormat",
+ "doi",
+ "sourceUrl",
+ "content"
+ ],
+ "type": "object"
+ }
+]Output schema / properties / deferred / properties / doisAdded value: +{
+ "description": "The deferred ids sent as DOIs, in response order — re-submit them as `dois`. Present only when the deferred ids came from more than one field (so `idType` is absent) and one of them was a DOI.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+}Output schema / properties / deferred / properties / idType / descriptionPrevious value: -"Which input branch the deferred ids belong to — re-submit them as `pmids`, `pmcids`, or `dois` respectively. Matches the `idType` on `unavailable` entries."New value: +"The input field every deferred id was sent in — re-submit them as `pmids`, `pmcids`, or `dois` respectively. Matches the `idType` on `unavailable` entries. Absent when the deferred ids came from more than one field; `pmcids` / `pmids` / `dois` then group them."Output schema / properties / deferred / properties / ids / descriptionPrevious value: -"Identifiers of the deferred articles, in response order, keyed as they were requested (PMC IDs in `PMC<digits>` form). Re-call `pubmed_fetch_fulltext` with these under the `idType` branch and the same other inputs. Never contains an id from `unavailable`."New value: +"Identifiers of the deferred articles, in response order, keyed as they were requested (PMC IDs in `PMC<digits>` form). Re-call `pubmed_fetch_fulltext` with these under the `idType` field — or, when `idType` is absent, with the `pmcids` / `pmids` / `dois` lists below — and the same other inputs. Never contains an id from `unavailable`."Output schema / properties / deferred / properties / pmcidsAdded value: +{
+ "description": "The deferred ids sent as PMC IDs, in response order — re-submit them as `pmcids`. Present only when the deferred ids came from more than one field (so `idType` is absent) and one of them was a PMC ID.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+}Output schema / properties / deferred / properties / pmidsAdded value: +{
+ "description": "The deferred ids sent as PMIDs, in response order — re-submit them as `pmids`. Present only when the deferred ids came from more than one field (so `idType` is absent) and one of them was a PMID.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+}Output schema / properties / deferred / requiredPrevious value: -[
- "maxResponseCharacters",
- "returnedCharacters",
- "deferredCount",
- "idType",
- "ids",
- "nextDeferredCharacters"
-]New value: +[
+ "maxResponseCharacters",
+ "returnedCharacters",
+ "deferredCount",
+ "ids",
+ "nextDeferredCharacters"
+]Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_filter`: A `sections` element holds no visible character — only whitespace, or invisible characters such as a zero-width space — so it names no heading. An exactly-empty element is not blank here; it is skipped. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_rate_limited",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_rate_limited",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "blank_filter"
+]Output schema / properties / unavailable / descriptionPrevious value: -"Per-identifier explanations for any requested PMIDs, PMCIDs, or DOIs with no returnable full text. `idType` discriminates which branch the id came from. Distinct from `deferred`: nothing here is retrievable by re-calling, and an id never appears in both."New value: +"Per-identifier explanations for any requested PMIDs, PMCIDs, or DOIs with no returnable full text. `idType` names the field each id was sent in. Distinct from `deferred`: nothing here is retrievable by re-calling, and an id never appears in both."Output schema / properties / unavailable / items / properties / idType / descriptionPrevious value: -"Which input branch the id came from"New value: +"Which input field the id was sent in — `pmids`, `pmcids`, or `dois` respectively"pubmed_find_related1 field changedOutput schema / properties / articles / items / properties / pubDate / descriptionPrevious value: -"Publication date"New value: +"Publication date as YYYY-MM-DD; a month- or year-only date reads as the first day of that month or year. On an NCBI Bookshelf chapter (`docType` \"chapter\") it is the chapter's own date — its last revision, otherwise its contribution — not the year its book began."pubmed_lookup_citation7 fields changedInput schema / properties / citations / items / descriptionPrevious value: -"Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match."New value: +"Citation to match against PubMed. Must include at least journal or a four-digit year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match."Input schema / properties / citations / items / properties / authorName / descriptionPrevious value: -"Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break."New value: +"Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Must contain a visible character, and cannot contain a pipe (\"|\") or a line break."Input schema / properties / citations / items / properties / firstPage / descriptionPrevious value: -"First page number. Cannot contain a pipe (\"|\") or a line break."New value: +"First page number. Must contain a visible character, and cannot contain a pipe (\"|\") or a line break."Input schema / properties / citations / items / properties / journal / descriptionPrevious value: -"Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break."New value: +"Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Must contain a visible character, and cannot contain a pipe (\"|\") or a line break."Input schema / properties / citations / items / properties / volume / descriptionPrevious value: -"Volume number. Cannot contain a pipe (\"|\") or a line break."New value: +"Volume number. Must contain a visible character, and cannot contain a pipe (\"|\") or a line break."Input schema / properties / citations / items / properties / year / descriptionPrevious value: -"Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break."New value: +"Publication year as four digits (e.g., \"1991\")."Input schema / properties / citations / items / properties / year / patternPrevious value: -"^[^|\\r\\n]*$"New value: +"^[ \\t]*\\d{4}[ \\t]*$"pubmed_search_articles5 fields changedInput schema / properties / dateRange / properties / maxDate / descriptionPrevious value: -"End date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound. Must be a real calendar date — `2023/02/29` is rejected."New value: +"End date (YYYY/MM/DD, YYYY/MM, or YYYY). Must be a real calendar date — `2023/02/29` is rejected. Leaving it empty drops the whole date range, not just this bound; for no upper bound pass a wide sentinel such as `3000`."Input schema / properties / dateRange / properties / minDate / descriptionPrevious value: -"Start date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound. Must be a real calendar date — `2023/02/29` is rejected."New value: +"Start date (YYYY/MM/DD, YYYY/MM, or YYYY). Must be a real calendar date — `2023/02/29` is rejected. Leaving it empty drops the whole date range, not just this bound; for no lower bound pass a wide sentinel such as `1000`."Input schema / properties / maxResults / descriptionPrevious value: -"Maximum results to return"New value: +"Maximum results to return. 0 returns only `totalCount`."Input schema / properties / maxResults / minimumPrevious value: -1New value: +0Output schema / properties / summaries / items / properties / pubDate / descriptionPrevious value: -"Publication date"New value: +"Publication date as YYYY-MM-DD; a month- or year-only date reads as the first day of that month or year. On an NCBI Bookshelf chapter (`docType` \"chapter\") it is the chapter's own date — its last revision, otherwise its contribution — not the year its book began."pubmed_convert_ids2 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found",
- "malformed_id"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_rate_limited",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "malformed_id"
+]pubmed_europepmc_fetch1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt. `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."pubmed_europepmc_search4 fields changedInput schema / properties / cursorMark / descriptionPrevious value: -"Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` for subsequent pages."New value: +"Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` verbatim for subsequent pages. A whitespace-only cursor, invisible characters included, is rejected before the request, and a cursor Europe PMC cannot read fails with `europepmc_invalid_input` once a retry of it fails again while the first page of the same query is served."Input schema / properties / query / descriptionPrevious value: -"Europe PMC search query. Supports field tokens like `AUTH:\"<name>\"`, `JOURNAL:\"<title>\"`, `TITLE:\"<words>\"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:\"...\"`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens may be quoted or unquoted — this tool wraps every query with its `sources` filter, and Europe PMC honors a quoted identifier inside that wrapper. A PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`, whichever identifier is used. Free text is matched broadly across abstract/title/keywords."New value: +"Europe PMC search query. Supports field tokens like `AUTH:\"<name>\"`, `JOURNAL:\"<title>\"`, `TITLE:\"<words>\"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:\"...\"`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens may be quoted or unquoted — this tool wraps every query with its `sources` filter, and Europe PMC honors a quoted identifier inside that wrapper. A PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`, whichever identifier is used. Free text is matched broadly across abstract/title/keywords. A query with no search term — blank once HTML entities are decoded and markup, parentheses, and invisible characters are disregarded, such as `()` or `<b></b>` — is rejected; any other query is sent as written."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt. `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message in place of results, an empty response to a sort with an undocumented field or no asc/desc direction, or a pagination cursor it cannot read (an empty response on the last attempt the retry budget allows, or a second HTTP 503 when the first page of the same query is served). `blank_query`: The query contains no search term: nothing is left once whitespace and invisible characters such as a zero-width space are disregarded. pubmed_search_articles and pubmed_europepmc_search first decode HTML entities and also disregard markup and parentheses, so `()`, `<b></b>`, and ` ` hold no term there; pubmed_search_articles also disregards bracketed field tags such as `[pdat]`. `blank_cursor`: The `cursorMark` holds only whitespace or invisible characters such as a zero-width space. Europe PMC cannot read it and answers with the HTTP 503 it also uses for an outage. `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "europepmc_unreachable",
- "europepmc_invalid_response",
- "europepmc_invalid_input",
- "europepmc_disabled"
-]New value: +[
+ "europepmc_unreachable",
+ "europepmc_invalid_response",
+ "europepmc_invalid_input",
+ "blank_query",
+ "blank_cursor",
+ "europepmc_disabled"
+]pubmed_fetch_articles3 fields changedOutput schema / properties / articles / items / properties / commentsCorrectionsAdded value: +{
+ "description": "Records NCBI links to this article — for example retraction notices, errata, expressions of concern, comments, and updates — from `CommentsCorrectionsList`, in NCBI's order and uncapped. `Cites` entries are excluded: they list a bibliography, which `pubmed_find_related` covers with its `references` relationship. Read this alongside `publicationTypes`, not in place of it: that field describes the record itself, and a corrected or questioned article often carries no matching type. Absent when NCBI links nothing other than `Cites` entries, and never set on `book-chapter` or `book` records.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One record NCBI links to this article and published separately from it — for example a retraction notice, erratum, expression of concern, comment, update, or republication.",
+ "properties": {
+ "note": {
+ "description": "NCBI's note on the link, e.g. what an erratum corrected (\"Fuβer, Fabian [corrected to Fußer, Fabian]\"). Absent unless NCBI supplies one.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PMID of the linked record — pass it to `pubmed_fetch_articles` to read that record. Absent when the linked record has no PMID, as with many errata.",
+ "type": "string"
+ },
+ "refSource": {
+ "description": "Citation of the linked record as NCBI writes it (e.g. \"Lancet. 2010 Feb 6;375(9713):445. doi: 10.1016/S0140-6736(10)60175-4.\").",
+ "type": "string"
+ },
+ "refType": {
+ "description": "Link type, verbatim from NCBI's `RefType` — e.g. \"RetractionIn\", \"RetractionOf\", \"ErratumIn\", \"ErratumFor\", \"ExpressionOfConcernIn\", \"CommentIn\", \"CommentOn\", \"UpdateIn\". The set is open: treat an unfamiliar value as opaque.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "refType",
+ "refSource"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+}Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `invalid_efetch_response`: NCBI EFetch returned a payload missing the PubmedArticleSet wrapper. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `invalid_efetch_response`: NCBI EFetch returned a payload missing the PubmedArticleSet wrapper. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found",
- "invalid_efetch_response"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_rate_limited",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "invalid_efetch_response"
+]pubmed_fetch_fulltext2 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_rate_limited",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+]pubmed_format_citations2 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_rate_limited",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+]pubmed_lookup_citation8 fields changedInput schema / properties / citations / anyOfRemoved value: -[
- {
- "description": "Up to 25 citations, each matched independently.",
- "items": {
- "description": "Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.",
- "properties": {
- "authorName": {
- "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "firstPage": {
- "description": "First page number. Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "journal": {
- "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "key": {
- "description": "Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.",
- "type": "string"
- },
- "volume": {
- "description": "Volume number. Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "year": {
- "description": "Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- }
- },
- "type": "object"
- },
- "maxItems": 25,
- "minItems": 1,
- "type": "array"
- },
- {
- "description": "Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.",
- "properties": {
- "authorName": {
- "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "firstPage": {
- "description": "First page number. Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "journal": {
- "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "key": {
- "description": "Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.",
- "type": "string"
- },
- "volume": {
- "description": "Volume number. Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "year": {
- "description": "Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- }
- },
- "type": "object"
- }
-]Input schema / properties / citations / descriptionPrevious value: -"Citations to look up — an array of up to 25, or a single citation object. More fields = better match accuracy."New value: +"Citations to look up, 1–25, each matched independently. More fields = better match accuracy."Input schema / properties / citations / itemsAdded value: +{
+ "description": "Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.",
+ "properties": {
+ "authorName": {
+ "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "firstPage": {
+ "description": "First page number. Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "journal": {
+ "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "key": {
+ "description": "Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number. Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ }
+ },
+ "type": "object"
+}Input schema / properties / citations / maxItemsAdded value: +25Input schema / properties / citations / minItemsAdded value: +1Input schema / properties / citations / typeAdded value: +"array"Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_rate_limited",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+]pubmed_lookup_mesh3 fields changedInput schema / properties / query / descriptionPrevious value: -"MeSH descriptor name or free-text term to look up. Must carry a term: a blank or whitespace-only value is rejected rather than searched."New value: +"MeSH descriptor name or free-text term to look up. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than searched."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query contains no search term: nothing is left once whitespace and invisible characters such as a zero-width space are disregarded. pubmed_search_articles and pubmed_europepmc_search first decode HTML entities and also disregard markup and parentheses, so `()`, `<b></b>`, and ` ` hold no term there; pubmed_search_articles also disregards bracketed field tags such as `[pdat]`. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found",
- "blank_query"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_rate_limited",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "blank_query"
+]pubmed_search_articles11 fields changedInput schema / properties / author / descriptionPrevious value: -"Filter by author name (e.g. \"Smith J\")"New value: +"Filter by author name (e.g. \"Smith J\"). An empty string applies no filter; a value of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected."Input schema / properties / dateRange / descriptionPrevious value: -"Filter by date range. The filter is applied only when both `minDate` and `maxDate` are non-empty; either one empty disables the entire date range."New value: +"Filter by date range. The filter is applied only when both `minDate` and `maxDate` are non-empty; either one empty disables the entire date range. A partial date covers its whole year or month, and a range whose `minDate` falls after its `maxDate` is rejected: `2024/06` to `2024` is valid, `2024/07` to `2024/06/30` is not."Input schema / properties / dateRange / properties / maxDate / descriptionPrevious value: -"End date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound"New value: +"End date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound. Must be a real calendar date — `2023/02/29` is rejected."Input schema / properties / dateRange / properties / minDate / descriptionPrevious value: -"Start date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound"New value: +"Start date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound. Must be a real calendar date — `2023/02/29` is rejected."Input schema / properties / journal / descriptionPrevious value: -"Filter by journal name"New value: +"Filter by journal name. An empty string applies no filter; a value of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected."Input schema / properties / language / descriptionPrevious value: -"Filter by language (e.g. \"english\")"New value: +"Filter by language (e.g. \"english\"). An empty string applies no filter; a value of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected."Input schema / properties / meshTerms / descriptionPrevious value: -"Filter by MeSH terms. Multiple terms are AND'd — all must match."New value: +"Filter by MeSH terms. Multiple terms are AND'd — all must match. Empty strings are skipped; an element of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected."Input schema / properties / publicationTypes / descriptionPrevious value: -"Filter by publication type (e.g. \"Review\", \"Clinical Trial\", \"Meta-Analysis\"). Multiple values are OR'd — any match qualifies."New value: +"Filter by publication type (e.g. \"Review\", \"Clinical Trial\", \"Meta-Analysis\"). Multiple values are OR'd — any match qualifies. Empty strings are skipped; an element of only whitespace, invisible characters, markup, parentheses, brackets, or double quotes is rejected."Input schema / properties / query / descriptionPrevious value: -"PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup, bracketed field tags (`[pdat]`), and parentheses are removed is rejected rather than sent to PubMed as an empty term."New value: +"PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup, bracketed field tags (`[pdat]`), parentheses, and invisible characters such as a zero-width space are disregarded is rejected rather than sent to PubMed."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query contains no search term: nothing is left once whitespace and invisible characters such as a zero-width space are disregarded. pubmed_search_articles and pubmed_europepmc_search first decode HTML entities and also disregard markup and parentheses, so `()`, `<b></b>`, and ` ` hold no term there; pubmed_search_articles also disregards bracketed field tags such as `[pdat]`. `invalid_date_range`: A `dateRange` bound is not a real calendar date — a month outside 01–12, day 00, or a day past the end of its month such as `2023/02/29` — or `minDate` falls after `maxDate` once PubMed expands each partial date: `minDate` from the start of its year or month, `maxDate` to the end. `blank_filter`: An `author`, `journal`, or `language` value, or a `publicationTypes` or `meshTerms` element, holds no term once markup is removed and HTML entities are decoded — only whitespace, invisible characters such as a zero-width space, parentheses, brackets, or double quotes are left, as in `()` or `\"\"` — so its field clause would carry no term. An exactly-empty string is not blank here; it sets no filter. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found",
- "blank_query"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_rate_limited",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "blank_query",
+ "invalid_date_range",
+ "blank_filter"
+]pubmed_spell_check3 fields changedInput schema / properties / query / descriptionPrevious value: -"PubMed search query to spell-check. Must carry a term: a blank or whitespace-only value is rejected rather than sent to ESpell."New value: +"PubMed search query to spell-check. Must carry a term: a value of only whitespace or invisible characters, such as a zero-width space, is rejected rather than sent to ESpell."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities failed on every attempt the retry budget allowed — retries ran out, or the next backoff would overrun the total deadline. `ncbi_rate_limited`: NCBI answered HTTP 429 (too many requests) and the call stopped on it — retries ran out, the next backoff would overrun the total deadline, or the Retry-After NCBI named outlasts the time left or the 30-second backoff cap. `ncbi_deadline_exceeded`: The total NCBI request deadline expired before NCBI answered successfully — mid-request, while queued, or during a retry backoff. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query contains no search term: nothing is left once whitespace and invisible characters such as a zero-width space are disregarded. pubmed_search_articles and pubmed_europepmc_search first decode HTML entities and also disregard markup and parentheses, so `()`, `<b></b>`, and ` ` hold no term there; pubmed_search_articles also disregards bracketed field tags such as `[pdat]`. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found",
- "blank_query"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_rate_limited",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "blank_query"
+]pubmed_fetch_fulltext10 fields changedInput schema / properties / maxCharacters / descriptionPrevious value: -"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text — which carries the inline blocks the parser renders in place, such as lists, definition lists, block quotes, boxed text, preformatted blocks and displayed formulae — plus table label, caption, cell and footnote text and asset label, caption and `href` text; or the `source=unpaywall` `content` body. Titles, abstracts, identifiers, and references are never counted or shortened. The counted unit is that text alone — the Markdown grid `content[]` renders around the cells (pipes, padding, the divider row, headings) is scaffolding this budget does not measure, so a table renders longer than it costs here. Sections are served first, then tables, then assets, each spending what is left, in document order — admission stops at the first entry that does not fit, and every entry from there on is dropped whole rather than cut mid-row or returned with a shortened caption, counted in `truncation.omittedTables` / `truncation.omittedAssets` and named in `truncation.articles[].omittedTableNames` / `omittedAssetNames`. Applied after `sections`, `maxSections`, `includeReferences`, `includeTables`, and `includeAssets`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body."New value: +"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text — which carries the inline blocks the parser renders in place, such as lists, definition lists, block quotes, boxed text, preformatted blocks and displayed formulae — plus table label, caption, cell and footnote text and asset label, caption and `href` text; or the `source=unpaywall` `content` body. Titles, abstracts, identifiers, and references are never counted or shortened. Shortened text ends at the last word boundary inside its allowance, so it can come back a few characters under it. The counted unit is that text alone — the Markdown grid `content[]` renders around the cells (pipes, padding, the divider row, headings) is scaffolding this budget does not measure, so a table renders longer than it costs here. Sections are served first, then tables, then assets, each spending what is left, in document order — admission stops at the first entry that does not fit, and every entry from there on is dropped whole rather than cut mid-row or returned with a shortened caption, counted in `truncation.omittedTables` / `truncation.omittedAssets` and named in `truncation.articles[].omittedTableNames` / `omittedAssetNames`. Applied after `sections`, `maxSections`, `includeReferences`, `includeTables`, and `includeAssets`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body."Input schema / properties / overflowMode / descriptionPrevious value: -"How to spend `maxCharacters` across an article that exceeds it. truncate: fill sections in document order, so early sections stay whole and sections past the budget are dropped (counted in `truncation.omittedSections`). outline: split the budget evenly so every section keeps its heading, and an excerpt as far as the budget reaches — use it to survey what an article contains before requesting specific `sections`. Ignored when no budget is set, and identical for `source=unpaywall` bodies, which have no headings to preserve."New value: +"How to spend `maxCharacters` across an article that exceeds it. truncate: fill sections in document order, so early sections stay whole, the section the budget runs out in is cut, and every section or subsection past that point is dropped (counted in `truncation.omittedSections`). outline: split the budget evenly so every section and subsection keeps its heading, and an excerpt as far as the budget reaches — a heading the budget left empty is marked as such in the rendered text. Use it to survey what an article contains before requesting specific `sections`. Ignored when no budget is set, and identical for `source=unpaywall` bodies, which have no headings to preserve."Output schema / properties / articles / items / oneOfPrevious value: -[
- {
- "additionalProperties": false,
- "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
- "properties": {
- "abstract": {
- "description": "Abstract",
- "type": "string"
- },
- "affiliations": {
- "description": "Author affiliations",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "articleType": {
- "description": "Article type",
- "type": "string"
- },
- "assets": {
- "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from the body leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One figure or supplementary-material item, with its caption, pointer, and section",
- "properties": {
- "assetType": {
- "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
- "enum": [
- "figure",
- "supplementary-material"
- ],
- "type": "string"
- },
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "href": {
- "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
- "type": "string"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Display label as printed, e.g. `Fig. 1`",
- "type": "string"
- },
- "sectionTitle": {
- "description": "Title of the innermost section enclosing the asset, wherever that section sits — body, `<back>` matter, or an appendix all count. Absent for an asset inside no section at all, such as a `<floats-group>` deposit.",
- "type": "string"
- }
- },
- "required": [
- "assetType"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "authors": {
- "description": "Authors",
- "items": {
- "additionalProperties": false,
- "description": "Author entry",
- "properties": {
- "collectiveName": {
- "description": "Group name",
- "type": "string"
- },
- "givenNames": {
- "description": "Given names",
- "type": "string"
- },
- "lastName": {
- "description": "Last name",
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "doi": {
- "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
- "type": "string"
- },
- "epmcId": {
- "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
- "type": "string"
- },
- "epmcSource": {
- "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
- "type": "string"
- },
- "journal": {
- "additionalProperties": false,
- "description": "Journal information",
- "properties": {
- "elocationId": {
- "description": "Electronic article locator from JATS `<elocation-id>` — the publisher-assigned article number (e.g. \"e20542\"). Journals that assign article numbers deposit no `<fpage>`, so this is the only locator on roughly half of PMC records. Never a substitute for `pages`; JATS carries no type attribute, so there is no counterpart to the `elocationIdType` that `pubmed_fetch_articles` reports.",
- "type": "string"
- },
- "issn": {
- "description": "ISSN",
- "type": "string"
- },
- "issue": {
- "description": "Issue number",
- "type": "string"
- },
- "pages": {
- "description": "Page range",
- "type": "string"
- },
- "title": {
- "description": "Journal title",
- "type": "string"
- },
- "volume": {
- "description": "Volume number",
- "type": "string"
- }
- },
- "type": "object"
- },
- "keywords": {
- "description": "Keywords",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "pmcId": {
- "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
- "type": "string"
- },
- "pmcUrl": {
- "description": "PMC URL — derived from `pmcId` when present",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID",
- "type": "string"
- },
- "publicationDate": {
- "additionalProperties": false,
- "description": "Publication date",
- "properties": {
- "day": {
- "description": "Publication day",
- "type": "string"
- },
- "month": {
- "description": "Publication month",
- "type": "string"
- },
- "year": {
- "description": "Publication year",
- "type": "string"
- }
- },
- "type": "object"
- },
- "pubmedUrl": {
- "description": "PubMed URL",
- "type": "string"
- },
- "references": {
- "description": "Reference list",
- "items": {
- "additionalProperties": false,
- "description": "Reference entry",
- "properties": {
- "citation": {
- "description": "Citation text",
- "type": "string"
- },
- "id": {
- "description": "Reference ID",
- "type": "string"
- },
- "label": {
- "description": "Reference label",
- "type": "string"
- }
- },
- "required": [
- "citation"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "sections": {
- "description": "Article body sections",
- "items": {
- "additionalProperties": false,
- "description": "Article body section",
- "properties": {
- "label": {
- "description": "Section label",
- "type": "string"
- },
- "subsections": {
- "description": "Nested subsections",
- "items": {
- "additionalProperties": false,
- "description": "Article subsection",
- "properties": {
- "label": {
- "description": "Subsection label",
- "type": "string"
- },
- "text": {
- "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
- "type": "string"
- },
- "title": {
- "description": "Subsection heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "text": {
- "description": "Section body text",
- "type": "string"
- },
- "title": {
- "description": "Section heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "source": {
- "const": "pmc",
- "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
- "type": "string"
- },
- "tables": {
- "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One table from the article, with its cells, caption, and owning section",
- "properties": {
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "footnotes": {
- "description": "`<table-wrap-foot>` text, flattened to one string",
- "type": "string"
- },
- "headerRowCount": {
- "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
- "type": "number"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Table label as printed, e.g. `TABLE 1`",
- "type": "string"
- },
- "rows": {
- "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. Empty when `unextractableReason` is set.",
- "items": {
- "description": "One row, as cell text by grid column",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "type": "array"
- },
- "sectionTitle": {
- "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
- "type": "string"
- },
- "unextractableReason": {
- "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
- "enum": [
- "cals-tgroup",
- "graphic-only",
- "no-rows"
- ],
- "type": "string"
- }
- },
- "required": [
- "headerRowCount",
- "rows"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "title": {
- "description": "Article title",
- "type": "string"
- },
- "viaSource": {
- "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
- "enum": [
- "pmc",
- "europepmc"
- ],
- "type": "string"
- }
- },
- "required": [
- "source",
- "viaSource",
- "sections"
- ],
- "type": "object"
- },
- {
- "additionalProperties": false,
- "description": "Best-effort full text from an open-access copy",
- "properties": {
- "content": {
- "description": "Full article text — Markdown or plain text per `contentFormat`",
- "type": "string"
- },
- "contentFormat": {
- "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
- "enum": [
- "html-markdown",
- "pdf-text"
- ],
- "type": "string"
- },
- "doi": {
- "description": "DOI used to locate the open-access copy",
- "type": "string"
- },
- "hostType": {
- "description": "`publisher` or `repository` — where the OA copy is hosted",
- "type": "string"
- },
- "license": {
- "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
- "type": "string"
- },
- "pmcId": {
- "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
- "type": "string"
- },
- "pubmedUrl": {
- "description": "PubMed URL — present when `pmid` is set",
- "type": "string"
- },
- "source": {
- "const": "unpaywall",
- "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
- "type": "string"
- },
- "sourceUrl": {
- "description": "URL the content was fetched from",
- "type": "string"
- },
- "title": {
- "description": "Detected article title when present",
- "type": "string"
- },
- "totalPages": {
- "description": "Page count reported by the PDF extractor; absent for HTML",
- "type": "number"
- },
- "version": {
- "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
- "type": "string"
- },
- "viaSource": {
- "const": "unpaywall",
- "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
- "type": "string"
- },
- "wordCount": {
- "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
- "type": "number"
- }
- },
- "required": [
- "source",
- "viaSource",
- "contentFormat",
- "doi",
- "sourceUrl",
- "content"
- ],
- "type": "object"
- }
-]New value: +[
+ {
+ "additionalProperties": false,
+ "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
+ "properties": {
+ "abstract": {
+ "description": "Abstract",
+ "type": "string"
+ },
+ "affiliations": {
+ "description": "Author affiliations",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "articleType": {
+ "description": "Article type",
+ "type": "string"
+ },
+ "assets": {
+ "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from the body leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One figure or supplementary-material item, with its caption, pointer, and section",
+ "properties": {
+ "assetType": {
+ "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
+ "enum": [
+ "figure",
+ "supplementary-material"
+ ],
+ "type": "string"
+ },
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "href": {
+ "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
+ "type": "string"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Display label as printed, e.g. `Fig. 1`",
+ "type": "string"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost section enclosing the asset, wherever that section sits — body, `<back>` matter, or an appendix all count. Absent for an asset inside no section at all, such as a `<floats-group>` deposit.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "assetType"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "authors": {
+ "description": "Authors",
+ "items": {
+ "additionalProperties": false,
+ "description": "Author entry",
+ "properties": {
+ "collectiveName": {
+ "description": "Group name",
+ "type": "string"
+ },
+ "givenNames": {
+ "description": "Given names",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Last name",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "doi": {
+ "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
+ "type": "string"
+ },
+ "epmcId": {
+ "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
+ "type": "string"
+ },
+ "epmcSource": {
+ "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
+ "type": "string"
+ },
+ "journal": {
+ "additionalProperties": false,
+ "description": "Journal information",
+ "properties": {
+ "elocationId": {
+ "description": "Electronic article locator from JATS `<elocation-id>` — the publisher-assigned article number (e.g. \"e20542\"). Journals that assign article numbers deposit no `<fpage>`, so this is the only locator on roughly half of PMC records. Never a substitute for `pages`; JATS carries no type attribute, so there is no counterpart to the `elocationIdType` that `pubmed_fetch_articles` reports.",
+ "type": "string"
+ },
+ "issn": {
+ "description": "ISSN",
+ "type": "string"
+ },
+ "issue": {
+ "description": "Issue number",
+ "type": "string"
+ },
+ "pages": {
+ "description": "Page range",
+ "type": "string"
+ },
+ "title": {
+ "description": "Journal title",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "keywords": {
+ "description": "Keywords",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "pmcId": {
+ "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
+ "type": "string"
+ },
+ "pmcUrl": {
+ "description": "PMC URL — derived from `pmcId` when present",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID",
+ "type": "string"
+ },
+ "publicationDate": {
+ "additionalProperties": false,
+ "description": "Publication date",
+ "properties": {
+ "day": {
+ "description": "Publication day",
+ "type": "string"
+ },
+ "month": {
+ "description": "Publication month",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL",
+ "type": "string"
+ },
+ "references": {
+ "description": "Reference list",
+ "items": {
+ "additionalProperties": false,
+ "description": "Reference entry",
+ "properties": {
+ "citation": {
+ "description": "Citation text",
+ "type": "string"
+ },
+ "id": {
+ "description": "Reference ID",
+ "type": "string"
+ },
+ "label": {
+ "description": "Reference label",
+ "type": "string"
+ }
+ },
+ "required": [
+ "citation"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "sections": {
+ "description": "Article body sections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article body section",
+ "properties": {
+ "label": {
+ "description": "Section label",
+ "type": "string"
+ },
+ "subsections": {
+ "description": "Nested subsections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article subsection",
+ "properties": {
+ "label": {
+ "description": "Subsection label",
+ "type": "string"
+ },
+ "text": {
+ "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
+ "type": "string"
+ },
+ "title": {
+ "description": "Subsection heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "text": {
+ "description": "Section body text",
+ "type": "string"
+ },
+ "title": {
+ "description": "Section heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "source": {
+ "const": "pmc",
+ "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
+ "type": "string"
+ },
+ "tables": {
+ "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One table from the article, with its cells, caption, and owning section",
+ "properties": {
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "footnotes": {
+ "description": "`<table-wrap-foot>` text, flattened to one string",
+ "type": "string"
+ },
+ "headerRowCount": {
+ "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
+ "type": "number"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Table label as printed, e.g. `TABLE 1`",
+ "type": "string"
+ },
+ "rows": {
+ "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. Empty when `unextractableReason` is set.",
+ "items": {
+ "description": "One row, as cell text by grid column",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "type": "array"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
+ "type": "string"
+ },
+ "unextractableReason": {
+ "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
+ "enum": [
+ "cals-tgroup",
+ "graphic-only",
+ "no-rows"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "headerRowCount",
+ "rows"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "title": {
+ "description": "Article title",
+ "type": "string"
+ },
+ "viaSource": {
+ "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
+ "enum": [
+ "pmc",
+ "europepmc"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "sections"
+ ],
+ "type": "object"
+ },
+ {
+ "additionalProperties": false,
+ "description": "Best-effort full text from an open-access copy",
+ "properties": {
+ "content": {
+ "description": "Full article text — Markdown or plain text per `contentFormat`",
+ "type": "string"
+ },
+ "contentFormat": {
+ "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
+ "enum": [
+ "html-markdown",
+ "pdf-text"
+ ],
+ "type": "string"
+ },
+ "doi": {
+ "description": "DOI used to locate the open-access copy",
+ "type": "string"
+ },
+ "hostType": {
+ "description": "`publisher` or `repository` — where the OA copy is hosted",
+ "type": "string"
+ },
+ "journalName": {
+ "description": "Journal or repository name from Unpaywall's record for the DOI (e.g. `medRxiv` for a medRxiv preprint). Absent when Unpaywall has none.",
+ "type": "string"
+ },
+ "license": {
+ "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
+ "type": "string"
+ },
+ "pmcId": {
+ "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
+ "type": "string"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL — present when `pmid` is set",
+ "type": "string"
+ },
+ "source": {
+ "const": "unpaywall",
+ "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
+ "type": "string"
+ },
+ "sourceUrl": {
+ "description": "URL the content was fetched from",
+ "type": "string"
+ },
+ "title": {
+ "description": "Article title, from the first source that carries one: Unpaywall's record for the DOI, then the Europe PMC record when the chain searched Europe PMC for this id, then — for `html-markdown` content only — the title detected on the page. Absent when none of them has a title.",
+ "type": "string"
+ },
+ "totalPages": {
+ "description": "Page count reported by the PDF extractor; absent for HTML",
+ "type": "number"
+ },
+ "version": {
+ "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
+ "type": "string"
+ },
+ "viaSource": {
+ "const": "unpaywall",
+ "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
+ "type": "string"
+ },
+ "wordCount": {
+ "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
+ "type": "number"
+ },
+ "year": {
+ "description": "Publication year from Unpaywall's record for the DOI. Absent when Unpaywall has none.",
+ "type": "number"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "contentFormat",
+ "doi",
+ "sourceUrl",
+ "content"
+ ],
+ "type": "object"
+ }
+]Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `unpaywall_unreachable`: Unpaywall was unreachable when resolving a DOI or fetching content. `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found",
- "unpaywall_unreachable",
- "europepmc_unreachable",
- "europepmc_invalid_response",
- "europepmc_invalid_input"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+]Output schema / properties / truncation / properties / articles / items / properties / sections / descriptionPrevious value: -"Per-section accounting for `source: pmc` articles, in document order, including sections dropped for budget. Absent for `source: unpaywall`, whose body has no section structure."New value: +"Per-section accounting for `source: pmc` articles, in document order, including sections dropped for budget; a shortened section lists its subsections. Absent for `source: unpaywall`, whose body has no section structure."Output schema / properties / truncation / properties / articles / items / properties / sections / items / properties / labelAdded value: +{
+ "description": "Section label as printed (e.g. `2`), when the section carries one",
+ "type": "string"
+}Output schema / properties / truncation / properties / articles / items / properties / sections / items / properties / returnedCharacters / descriptionPrevious value: -"Body characters this section carries in the response. Zero means the section was dropped in `truncate` mode, or kept as a heading-only entry in `outline` mode."New value: +"Body characters this section carries in the response. Zero means the section was dropped in `truncate` mode, or kept as a heading-only entry in `outline` mode, marked as such in the rendered text."Output schema / properties / truncation / properties / articles / items / properties / sections / items / properties / subsectionsAdded value: +{
+ "description": "Per-subsection accounting for a shortened section, in document order, including subsections dropped for budget — where inside the section the cut landed. Absent when the section was returned whole or carries no subsections.",
+ "items": {
+ "additionalProperties": false,
+ "description": "Character accounting for one subsection of a shortened section",
+ "properties": {
+ "label": {
+ "description": "Subsection label as printed (e.g. `2.1`), when the subsection carries one",
+ "type": "string"
+ },
+ "originalCharacters": {
+ "description": "Body characters this subsection carried before the budget pass",
+ "type": "number"
+ },
+ "returnedCharacters": {
+ "description": "Body characters this subsection carries in the response. Zero means it was dropped in `truncate` mode and counted in `omittedSections`, or kept as a heading-only entry in `outline` mode, marked as such in the rendered text.",
+ "type": "number"
+ },
+ "title": {
+ "description": "Subsection heading, when the subsection carries one",
+ "type": "string"
+ },
+ "truncated": {
+ "description": "True when the subsection returned fewer characters than it originally carried",
+ "type": "boolean"
+ }
+ },
+ "required": [
+ "originalCharacters",
+ "returnedCharacters",
+ "truncated"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+}Output schema / properties / truncation / properties / omittedSections / descriptionPrevious value: -"Body sections dropped entirely because an article budget was exhausted before reaching them. Always 0 in `outline` mode, which keeps every heading."New value: +"Body sections and subsections dropped entirely because an article budget was exhausted before reaching them. A dropped section counts once, together with its subsections. Always 0 in `outline` mode, which keeps every heading."pubmed_europepmc_search2 fields changedInput schema / properties / query / descriptionPrevious value: -"Europe PMC search query. Supports field tokens like `AUTH:\"<name>\"`, `JOURNAL:\"<title>\"`, `TITLE:\"<words>\"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:\"...\"`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens combined with `AND SRC:` must be unquoted — the quoted form matches nothing. Free text is matched broadly across abstract/title/keywords."New value: +"Europe PMC search query. Supports field tokens like `AUTH:\"<name>\"`, `JOURNAL:\"<title>\"`, `TITLE:\"<words>\"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:\"...\"`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens may be quoted or unquoted — this tool wraps every query with its `sources` filter, and Europe PMC honors a quoted identifier inside that wrapper. A PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`, whichever identifier is used. Free text is matched broadly across abstract/title/keywords."Output schema / anyOfPrevious value: -[
- {
- "not": {
- "required": [
- "error"
- ]
- },
- "required": [
- "hits",
- "cursorMark",
- "searchUrl",
- "query",
- "totalCount",
- "appliedSources"
- ]
- },
- {
- "required": [
- "error"
- ]
- }
-]New value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "hits",
+ "cursorMark",
+ "searchUrl",
+ "totalCount",
+ "query",
+ "appliedSources"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]pubmed_lookup_citation6 fields changedInput schema / properties / citations / anyOfAdded value: +[
+ {
+ "description": "Up to 25 citations, each matched independently.",
+ "items": {
+ "description": "Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.",
+ "properties": {
+ "authorName": {
+ "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "firstPage": {
+ "description": "First page number. Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "journal": {
+ "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "key": {
+ "description": "Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number. Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "maxItems": 25,
+ "minItems": 1,
+ "type": "array"
+ },
+ {
+ "description": "Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.",
+ "properties": {
+ "authorName": {
+ "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "firstPage": {
+ "description": "First page number. Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "journal": {
+ "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "key": {
+ "description": "Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number. Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break.",
+ "pattern": "^[^|\\r\\n]*$",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ }
+]Input schema / properties / citations / descriptionPrevious value: -"Citations to look up. More fields = better match accuracy."New value: +"Citations to look up — an array of up to 25, or a single citation object. More fields = better match accuracy."Input schema / properties / citations / itemsRemoved value: -{
- "description": "Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.",
- "properties": {
- "authorName": {
- "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "firstPage": {
- "description": "First page number. Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "journal": {
- "description": "Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "key": {
- "description": "Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.",
- "type": "string"
- },
- "volume": {
- "description": "Volume number. Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- },
- "year": {
- "description": "Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break.",
- "pattern": "^[^|\\r\\n]*$",
- "type": "string"
- }
- },
- "type": "object"
-}Input schema / properties / citations / maxItemsRemoved value: -25Input schema / properties / citations / minItemsRemoved value: -1Input schema / properties / citations / typeRemoved value: -"array"pubmed_lookup_mesh1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there. Other values are possible when a failure originates below the handler."pubmed_search_articles3 fields changedInput schema / properties / query / descriptionPrevious value: -"PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup is stripped is rejected rather than sent to PubMed as an empty term."New value: +"PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup, bracketed field tags (`[pdat]`), and parentheses are removed is rejected rather than sent to PubMed as an empty term."Output schema / anyOfPrevious value: -[
- {
- "not": {
- "required": [
- "error"
- ]
- },
- "required": [
- "query",
- "offset",
- "pmids",
- "summaries",
- "searchUrl",
- "effectiveQuery",
- "totalCount",
- "appliedFilters"
- ]
- },
- {
- "required": [
- "error"
- ]
- }
-]New value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "query",
+ "offset",
+ "pmids",
+ "summaries",
+ "searchUrl",
+ "totalCount",
+ "effectiveQuery",
+ "appliedFilters"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there. Other values are possible when a failure originates below the handler."pubmed_spell_check1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there. Other values are possible when a failure originates below the handler."pubmed_convert_ids1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."pubmed_europepmc_fetch1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt. `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."pubmed_europepmc_search2 fields changedInput schema / properties / sort / descriptionPrevious value: -"Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC. Note: `P_PDATE_D` is ignored for preprint-only (`sources: [\"PPR\"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date."New value: +"Optional EPMC sort: `<field> asc|desc`, or several comma-separated keys applied in order (`PUB_YEAR desc, CITED desc`). Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Field and direction match case-insensitively. A field outside the documented set may be honored, silently ignored, or rejected, and a sort using one — or a key without `asc`/`desc` — can fail with `europepmc_invalid_input` naming it, even when Europe PMC honors the field. Note: `P_PDATE_D` is ignored for preprint-only (`sources: [\"PPR\"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt. `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."pubmed_fetch_articles1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `invalid_efetch_response`: NCBI EFetch returned a payload missing the PubmedArticleSet wrapper. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `invalid_efetch_response`: NCBI EFetch returned a payload missing the PubmedArticleSet wrapper. Other values are possible when a failure originates below the handler."pubmed_fetch_fulltext1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `unpaywall_unreachable`: Unpaywall was unreachable when resolving a DOI or fetching content. `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `unpaywall_unreachable`: Unpaywall was unreachable when resolving a DOI or fetching content. `europepmc_unreachable`: Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt. Other values are possible when a failure originates below the handler."pubmed_find_related2 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `openalex_unreachable`: OpenAlex was unreachable after all retry attempts. `openalex_invalid_response`: OpenAlex returned a body that could not be parsed (invalid JSON). `all_providers_failed`: Every provider eligible for the requested relationship failed; none answered. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `all_providers_failed`: Every provider eligible for the requested relationship failed; none answered. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found",
- "europepmc_unreachable",
- "europepmc_invalid_response",
- "europepmc_invalid_input",
- "openalex_unreachable",
- "openalex_invalid_response",
- "all_providers_failed"
-]New value: +[
+ "all_providers_failed"
+]pubmed_format_citations1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."pubmed_lookup_citation1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."pubmed_lookup_mesh1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."pubmed_search_articles1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."pubmed_spell_check1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429). `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."pubmed_convert_ids3 fields changedInput schema / properties / ids / descriptionPrevious value: -"Article identifiers to convert. All IDs must be the same type. DOIs: \"10.1093/nar/gks1195\", PMIDs: \"23193287\", PMCIDs: \"PMC3531190\" (the \"PMC\" prefix is optional — bare digits like \"3531190\" are also accepted)."New value: +"Article identifiers to convert — one identifier per element, all of the same type. Each element is checked against `idType` before the request: `doi` starts with \"10.\" and carries a \"/\" (\"10.1093/nar/gks1195\"); `pmid` is digits (\"23193287\"); `pmcid` is digits with an optional \"PMC\" prefix (\"PMC3531190\" or \"3531190\"). No element may contain a comma or whitespace — a packed value like \"23193287,37952131\" is rejected, so split it across elements."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `malformed_id`: An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "malformed_id"
+]pubmed_fetch_articles9 fields changedOutput schema / properties / articles / items / properties / authors / descriptionPrevious value: -"Author list"New value: +"Author list. On a `book-chapter` these are the chapter's own authors, never the book's editors, which are in `book.editors`. Empty on a Bookshelf record that credits neither."Output schema / properties / articles / items / properties / bookAdded value: +{
+ "additionalProperties": false,
+ "description": "The containing book of a `book-chapter`, or the book itself on a `book` record. Present only on those two record types, and never a stand-in for `journalInfo`.",
+ "properties": {
+ "accession": {
+ "description": "NCBI Bookshelf accession from `ArticleIdList` (`bookaccession`), e.g. \"NBK1247\". The record is readable at `https://www.ncbi.nlm.nih.gov/books/<accession>/`.",
+ "type": "string"
+ },
+ "beginningDate": {
+ "description": "First year of a continuously-updated book, from `Book/BeginningDate` (GeneReviews runs from 1993). Absent on a book published once.",
+ "type": "string"
+ },
+ "collectionTitle": {
+ "description": "Series the book belongs to, from `Book/CollectionTitle` (e.g. \"ADA Clinical Compendia Series\"). Absent for a book outside a series.",
+ "type": "string"
+ },
+ "doi": {
+ "description": "The book's own DOI, from `Book/ELocationID` with `EIdType=\"doi\"`. Distinct from the record-level `doi`, which is the chapter's: a chapter does not inherit this one.",
+ "type": "string"
+ },
+ "edition": {
+ "description": "Edition statement from `Book/Edition`. Rare on Bookshelf titles — absent unless NCBI supplies one.",
+ "type": "string"
+ },
+ "editors": {
+ "description": "Editors of the containing book, from `Book/AuthorList` marked `Type=\"editors\"`. Kept out of `authors`, which carries the chapter's own writers. Absent when the book credits no editors.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One editor of the containing book. Name parts only — editors are a citation credit, not a contributor record, so no affiliations or ORCID are reported for them.",
+ "properties": {
+ "collectiveName": {
+ "description": "Group or committee credited as editor, when the entry names an organization rather than a person. Mutually exclusive with the name-part fields.",
+ "type": "string"
+ },
+ "firstName": {
+ "description": "Editor given name as NCBI supplies it (`ForeName`, often \"Margaret P\"). Absent when NCBI carries initials only, or on a group editor.",
+ "type": "string"
+ },
+ "initials": {
+ "description": "Editor initials with no separators (e.g. \"MP\"). Absent when NCBI supplies none, or on a group editor.",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Editor surname, from the book's `Book/AuthorList Type=\"editors\"` entry. Absent on a group editor, which carries `collectiveName` instead.",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "endingDate": {
+ "description": "Last year of a closed date range, from `Book/EndingDate`. Absent while a book is still being updated, which leaves the range open-ended.",
+ "type": "string"
+ },
+ "isbns": {
+ "description": "Every `Book/Isbn` on the record. A book commonly carries a print and an electronic ISBN, so this is a list. Absent for a Bookshelf title with no ISBN, which is most of them.",
+ "items": {
+ "description": "One ISBN, verbatim as NCBI reports it — leading zeros intact",
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "medium": {
+ "description": "Medium the book is published in, from `Book/Medium` — \"Internet\" wherever NCBI supplies it. Absent when NCBI supplies none; it is never defaulted.",
+ "type": "string"
+ },
+ "pubDate": {
+ "description": "Publication year from `Book/PubDate`. Year only — NCBI's month and day are not reported, since no citation style uses them for a book.",
+ "type": "string"
+ },
+ "publisher": {
+ "description": "Publisher of the book, from `Book/Publisher/PublisherName`.",
+ "type": "string"
+ },
+ "publisherLocation": {
+ "description": "Place of publication, from `Book/Publisher/PublisherLocation` (e.g. \"Seattle (WA)\"). Absent when NCBI supplies no place.",
+ "type": "string"
+ },
+ "title": {
+ "description": "Title of the containing book, from `Book/BookTitle` (e.g. \"GeneReviews®\"). On a `book` record this is the same value as the record's own `title`.",
+ "type": "string"
+ }
+ },
+ "type": "object"
+}Output schema / properties / articles / items / properties / journalInfo / descriptionPrevious value: -"Journal information"New value: +"Journal information. Present on `journal-article` records only — absent on `book-chapter` and `book` records, because a Bookshelf record has no journal and its book title is never reported as one; read `book` for those. (#114)"Output schema / properties / articles / items / properties / journalInfo / properties / elocationIdAdded value: +{
+ "description": "Electronic article locator from NCBI `ELocationID` — the publisher-assigned article number (e.g. \"2400512\"). Journals that assign article numbers instead of pages often omit pagination entirely, leaving this the only locator. Never a substitute for `pages`, and never the DOI: a DOI-typed `ELocationID` is reported in `doi` instead. Absent when the only locator NCBI supplies is marked invalid.",
+ "type": "string"
+}Output schema / properties / articles / items / properties / journalInfo / properties / elocationIdTypeAdded value: +{
+ "description": "Type of `elocationId`, from NCBI's `EIdType` attribute — \"pii\" in practice. Free-form: NCBI does not close the set, so treat an unfamiliar value as opaque.",
+ "type": "string"
+}Output schema / properties / articles / items / properties / recordTypeAdded value: +{
+ "description": "Which kind of PubMed record this is, set from the XML element it arrived in: `journal-article` for an ordinary article, `book-chapter` for an NCBI Bookshelf chapter, `book` for a whole Bookshelf book. Read this to tell the three apart — `publicationTypes` cannot, because PubMed labels a Bookshelf record \"Review\" or \"Study Guide\". `journalInfo` is present only on `journal-article`; `book` only on the other two.",
+ "enum": [
+ "journal-article",
+ "book-chapter",
+ "book"
+ ],
+ "type": "string"
+}Output schema / properties / articles / items / properties / title / descriptionPrevious value: -"Article title"New value: +"Article title — the chapter title on a `book-chapter`, and the book title on a `book` record, where it repeats `book.title`."Output schema / properties / articles / items / requiredAdded value: +[
+ "recordType"
+]Output schema / properties / unavailablePmids / descriptionPrevious value: -"PMIDs that returned no article data. Reported in full regardless of where a `maxResponseCharacters` cutoff lands — these are misses, not deferrals, and re-requesting them returns nothing."New value: +"PMIDs PubMed returned no record for. That is all this reports: PubMed omits an unknown PMID silently, with no error and no reason, so the absence says nothing about whether the PMID exists. Reported in full regardless of where a `maxResponseCharacters` cutoff lands — these are misses, not deferrals. Use `pubmed_search_articles` to find PMIDs that do resolve."pubmed_fetch_fulltext4 fields changedInput schema / properties / dois / descriptionPrevious value: -"DOIs to resolve (e.g. [\"10.21203/rs.3.rs-9010375/v1\"]). Provide exactly one of `pmcids`, `pmids`, or `dois`. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled."New value: +"DOIs to resolve (e.g. [\"10.21203/rs.3.rs-9010375/v1\"]), one per element. Provide exactly one of `pmcids`, `pmids`, or `dois`. Resolved to a PMCID via the PMC ID Converter and returned as structured JATS when the article is in PMC; DOIs with no PMC counterpart (preprints, EPMC-only OA) fall through to Europe PMC, then Unpaywall, when those layers are enabled."Input schema / properties / dois / items / minLengthRemoved value: -3Input schema / properties / dois / items / patternAdded value: +"^10\\.[^\\s,]+\\/[^\\s,]+$"Output schema / properties / articles / items / oneOfPrevious value: -[
- {
- "additionalProperties": false,
- "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
- "properties": {
- "abstract": {
- "description": "Abstract",
- "type": "string"
- },
- "affiliations": {
- "description": "Author affiliations",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "articleType": {
- "description": "Article type",
- "type": "string"
- },
- "assets": {
- "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from the body leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One figure or supplementary-material item, with its caption, pointer, and section",
- "properties": {
- "assetType": {
- "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
- "enum": [
- "figure",
- "supplementary-material"
- ],
- "type": "string"
- },
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "href": {
- "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
- "type": "string"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Display label as printed, e.g. `Fig. 1`",
- "type": "string"
- },
- "sectionTitle": {
- "description": "Title of the innermost section enclosing the asset, wherever that section sits — body, `<back>` matter, or an appendix all count. Absent for an asset inside no section at all, such as a `<floats-group>` deposit.",
- "type": "string"
- }
- },
- "required": [
- "assetType"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "authors": {
- "description": "Authors",
- "items": {
- "additionalProperties": false,
- "description": "Author entry",
- "properties": {
- "collectiveName": {
- "description": "Group name",
- "type": "string"
- },
- "givenNames": {
- "description": "Given names",
- "type": "string"
- },
- "lastName": {
- "description": "Last name",
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "doi": {
- "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
- "type": "string"
- },
- "epmcId": {
- "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
- "type": "string"
- },
- "epmcSource": {
- "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
- "type": "string"
- },
- "journal": {
- "additionalProperties": false,
- "description": "Journal information",
- "properties": {
- "issn": {
- "description": "ISSN",
- "type": "string"
- },
- "issue": {
- "description": "Issue number",
- "type": "string"
- },
- "pages": {
- "description": "Page range",
- "type": "string"
- },
- "title": {
- "description": "Journal title",
- "type": "string"
- },
- "volume": {
- "description": "Volume number",
- "type": "string"
- }
- },
- "type": "object"
- },
- "keywords": {
- "description": "Keywords",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "pmcId": {
- "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
- "type": "string"
- },
- "pmcUrl": {
- "description": "PMC URL — derived from `pmcId` when present",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID",
- "type": "string"
- },
- "publicationDate": {
- "additionalProperties": false,
- "description": "Publication date",
- "properties": {
- "day": {
- "description": "Publication day",
- "type": "string"
- },
- "month": {
- "description": "Publication month",
- "type": "string"
- },
- "year": {
- "description": "Publication year",
- "type": "string"
- }
- },
- "type": "object"
- },
- "pubmedUrl": {
- "description": "PubMed URL",
- "type": "string"
- },
- "references": {
- "description": "Reference list",
- "items": {
- "additionalProperties": false,
- "description": "Reference entry",
- "properties": {
- "citation": {
- "description": "Citation text",
- "type": "string"
- },
- "id": {
- "description": "Reference ID",
- "type": "string"
- },
- "label": {
- "description": "Reference label",
- "type": "string"
- }
- },
- "required": [
- "citation"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "sections": {
- "description": "Article body sections",
- "items": {
- "additionalProperties": false,
- "description": "Article body section",
- "properties": {
- "label": {
- "description": "Section label",
- "type": "string"
- },
- "subsections": {
- "description": "Nested subsections",
- "items": {
- "additionalProperties": false,
- "description": "Article subsection",
- "properties": {
- "label": {
- "description": "Subsection label",
- "type": "string"
- },
- "text": {
- "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
- "type": "string"
- },
- "title": {
- "description": "Subsection heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "text": {
- "description": "Section body text",
- "type": "string"
- },
- "title": {
- "description": "Section heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "source": {
- "const": "pmc",
- "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
- "type": "string"
- },
- "tables": {
- "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One table from the article, with its cells, caption, and owning section",
- "properties": {
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "footnotes": {
- "description": "`<table-wrap-foot>` text, flattened to one string",
- "type": "string"
- },
- "headerRowCount": {
- "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
- "type": "number"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Table label as printed, e.g. `TABLE 1`",
- "type": "string"
- },
- "rows": {
- "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. Empty when `unextractableReason` is set.",
- "items": {
- "description": "One row, as cell text by grid column",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "type": "array"
- },
- "sectionTitle": {
- "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
- "type": "string"
- },
- "unextractableReason": {
- "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
- "enum": [
- "cals-tgroup",
- "graphic-only",
- "no-rows"
- ],
- "type": "string"
- }
- },
- "required": [
- "headerRowCount",
- "rows"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "title": {
- "description": "Article title",
- "type": "string"
- },
- "viaSource": {
- "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
- "enum": [
- "pmc",
- "europepmc"
- ],
- "type": "string"
- }
- },
- "required": [
- "source",
- "viaSource",
- "sections"
- ],
- "type": "object"
- },
- {
- "additionalProperties": false,
- "description": "Best-effort full text from an open-access copy",
- "properties": {
- "content": {
- "description": "Full article text — Markdown or plain text per `contentFormat`",
- "type": "string"
- },
- "contentFormat": {
- "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
- "enum": [
- "html-markdown",
- "pdf-text"
- ],
- "type": "string"
- },
- "doi": {
- "description": "DOI used to locate the open-access copy",
- "type": "string"
- },
- "hostType": {
- "description": "`publisher` or `repository` — where the OA copy is hosted",
- "type": "string"
- },
- "license": {
- "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
- "type": "string"
- },
- "pmcId": {
- "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
- "type": "string"
- },
- "pubmedUrl": {
- "description": "PubMed URL — present when `pmid` is set",
- "type": "string"
- },
- "source": {
- "const": "unpaywall",
- "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
- "type": "string"
- },
- "sourceUrl": {
- "description": "URL the content was fetched from",
- "type": "string"
- },
- "title": {
- "description": "Detected article title when present",
- "type": "string"
- },
- "totalPages": {
- "description": "Page count reported by the PDF extractor; absent for HTML",
- "type": "number"
- },
- "version": {
- "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
- "type": "string"
- },
- "viaSource": {
- "const": "unpaywall",
- "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
- "type": "string"
- },
- "wordCount": {
- "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
- "type": "number"
- }
- },
- "required": [
- "source",
- "viaSource",
- "contentFormat",
- "doi",
- "sourceUrl",
- "content"
- ],
- "type": "object"
- }
-]New value: +[
+ {
+ "additionalProperties": false,
+ "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
+ "properties": {
+ "abstract": {
+ "description": "Abstract",
+ "type": "string"
+ },
+ "affiliations": {
+ "description": "Author affiliations",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "articleType": {
+ "description": "Article type",
+ "type": "string"
+ },
+ "assets": {
+ "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from the body leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One figure or supplementary-material item, with its caption, pointer, and section",
+ "properties": {
+ "assetType": {
+ "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
+ "enum": [
+ "figure",
+ "supplementary-material"
+ ],
+ "type": "string"
+ },
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "href": {
+ "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
+ "type": "string"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Display label as printed, e.g. `Fig. 1`",
+ "type": "string"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost section enclosing the asset, wherever that section sits — body, `<back>` matter, or an appendix all count. Absent for an asset inside no section at all, such as a `<floats-group>` deposit.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "assetType"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "authors": {
+ "description": "Authors",
+ "items": {
+ "additionalProperties": false,
+ "description": "Author entry",
+ "properties": {
+ "collectiveName": {
+ "description": "Group name",
+ "type": "string"
+ },
+ "givenNames": {
+ "description": "Given names",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Last name",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "doi": {
+ "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
+ "type": "string"
+ },
+ "epmcId": {
+ "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
+ "type": "string"
+ },
+ "epmcSource": {
+ "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
+ "type": "string"
+ },
+ "journal": {
+ "additionalProperties": false,
+ "description": "Journal information",
+ "properties": {
+ "elocationId": {
+ "description": "Electronic article locator from JATS `<elocation-id>` — the publisher-assigned article number (e.g. \"e20542\"). Journals that assign article numbers deposit no `<fpage>`, so this is the only locator on roughly half of PMC records. Never a substitute for `pages`; JATS carries no type attribute, so there is no counterpart to the `elocationIdType` that `pubmed_fetch_articles` reports.",
+ "type": "string"
+ },
+ "issn": {
+ "description": "ISSN",
+ "type": "string"
+ },
+ "issue": {
+ "description": "Issue number",
+ "type": "string"
+ },
+ "pages": {
+ "description": "Page range",
+ "type": "string"
+ },
+ "title": {
+ "description": "Journal title",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "keywords": {
+ "description": "Keywords",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "pmcId": {
+ "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
+ "type": "string"
+ },
+ "pmcUrl": {
+ "description": "PMC URL — derived from `pmcId` when present",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID",
+ "type": "string"
+ },
+ "publicationDate": {
+ "additionalProperties": false,
+ "description": "Publication date",
+ "properties": {
+ "day": {
+ "description": "Publication day",
+ "type": "string"
+ },
+ "month": {
+ "description": "Publication month",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL",
+ "type": "string"
+ },
+ "references": {
+ "description": "Reference list",
+ "items": {
+ "additionalProperties": false,
+ "description": "Reference entry",
+ "properties": {
+ "citation": {
+ "description": "Citation text",
+ "type": "string"
+ },
+ "id": {
+ "description": "Reference ID",
+ "type": "string"
+ },
+ "label": {
+ "description": "Reference label",
+ "type": "string"
+ }
+ },
+ "required": [
+ "citation"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "sections": {
+ "description": "Article body sections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article body section",
+ "properties": {
+ "label": {
+ "description": "Section label",
+ "type": "string"
+ },
+ "subsections": {
+ "description": "Nested subsections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article subsection",
+ "properties": {
+ "label": {
+ "description": "Subsection label",
+ "type": "string"
+ },
+ "text": {
+ "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
+ "type": "string"
+ },
+ "title": {
+ "description": "Subsection heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "text": {
+ "description": "Section body text",
+ "type": "string"
+ },
+ "title": {
+ "description": "Section heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "source": {
+ "const": "pmc",
+ "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
+ "type": "string"
+ },
+ "tables": {
+ "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One table from the article, with its cells, caption, and owning section",
+ "properties": {
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "footnotes": {
+ "description": "`<table-wrap-foot>` text, flattened to one string",
+ "type": "string"
+ },
+ "headerRowCount": {
+ "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
+ "type": "number"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Table label as printed, e.g. `TABLE 1`",
+ "type": "string"
+ },
+ "rows": {
+ "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. Empty when `unextractableReason` is set.",
+ "items": {
+ "description": "One row, as cell text by grid column",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "type": "array"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
+ "type": "string"
+ },
+ "unextractableReason": {
+ "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
+ "enum": [
+ "cals-tgroup",
+ "graphic-only",
+ "no-rows"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "headerRowCount",
+ "rows"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "title": {
+ "description": "Article title",
+ "type": "string"
+ },
+ "viaSource": {
+ "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
+ "enum": [
+ "pmc",
+ "europepmc"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "sections"
+ ],
+ "type": "object"
+ },
+ {
+ "additionalProperties": false,
+ "description": "Best-effort full text from an open-access copy",
+ "properties": {
+ "content": {
+ "description": "Full article text — Markdown or plain text per `contentFormat`",
+ "type": "string"
+ },
+ "contentFormat": {
+ "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
+ "enum": [
+ "html-markdown",
+ "pdf-text"
+ ],
+ "type": "string"
+ },
+ "doi": {
+ "description": "DOI used to locate the open-access copy",
+ "type": "string"
+ },
+ "hostType": {
+ "description": "`publisher` or `repository` — where the OA copy is hosted",
+ "type": "string"
+ },
+ "license": {
+ "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
+ "type": "string"
+ },
+ "pmcId": {
+ "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
+ "type": "string"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL — present when `pmid` is set",
+ "type": "string"
+ },
+ "source": {
+ "const": "unpaywall",
+ "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
+ "type": "string"
+ },
+ "sourceUrl": {
+ "description": "URL the content was fetched from",
+ "type": "string"
+ },
+ "title": {
+ "description": "Detected article title when present",
+ "type": "string"
+ },
+ "totalPages": {
+ "description": "Page count reported by the PDF extractor; absent for HTML",
+ "type": "number"
+ },
+ "version": {
+ "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
+ "type": "string"
+ },
+ "viaSource": {
+ "const": "unpaywall",
+ "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
+ "type": "string"
+ },
+ "wordCount": {
+ "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
+ "type": "number"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "contentFormat",
+ "doi",
+ "sourceUrl",
+ "content"
+ ],
+ "type": "object"
+ }
+]pubmed_find_related6 fields changedOutput schema / properties / articles / items / properties / authors / descriptionPrevious value: -"Author string"New value: +"Author string — the first three of the record's own authors, then \"et al.\". On an NCBI Bookshelf chapter these are the chapter's authors; the book's editors are in `editors`."Output schema / properties / articles / items / properties / bookTitleAdded value: +{
+ "description": "Title of the book an NCBI Bookshelf record belongs to. Present instead of `source` on a book record; absent on a journal article.",
+ "type": "string"
+}Output schema / properties / articles / items / properties / docTypeAdded value: +{
+ "description": "What PubMed classifies this record as: \"chapter\" or \"book\" for an NCBI Bookshelf record, \"citation\" for an ordinary journal article. Absent when PubMed supplies none.",
+ "type": "string"
+}Output schema / properties / articles / items / properties / editorsAdded value: +{
+ "description": "Editors of the containing book, kept out of `authors` so they cannot displace the record's own authors. Absent on a journal article and on a book that credits no editors.",
+ "items": {
+ "description": "One editor, \"Surname Initials\" as ESummary renders it",
+ "type": "string"
+ },
+ "type": "array"
+}Output schema / properties / articles / items / properties / publisherNameAdded value: +{
+ "description": "Publisher of the book an NCBI Bookshelf record belongs to. Present only on a book record; absent on a journal article.",
+ "type": "string"
+}Output schema / properties / articles / items / properties / source / descriptionPrevious value: -"Journal source"New value: +"Journal the article appeared in. Absent on an NCBI Bookshelf record, which has no journal — its venue is in `bookTitle` and `publisherName` instead, and `docType` says which kind of record it is."pubmed_format_citations1 field changedOutput schema / properties / unavailablePmids / descriptionPrevious value: -"Requested PMIDs that did not return article metadata"New value: +"PMIDs PubMed returned no record for, so nothing could be cited for them. That is all this reports: PubMed omits a PMID it does not recognize silently, with no error and no reason, so the absence says nothing about whether the PMID exists. Use `pubmed_search_articles` to find PMIDs that do resolve."pubmed_lookup_citation11 fields changedInput schema / properties / citations / items / properties / authorName / descriptionPrevious value: -"Author name, typically \"lastname initials\" (e.g., \"mann bj\")"New value: +"Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break."Input schema / properties / citations / items / properties / authorName / patternAdded value: +"^[^|\\r\\n]*$"Input schema / properties / citations / items / properties / firstPage / descriptionPrevious value: -"First page number"New value: +"First page number. Cannot contain a pipe (\"|\") or a line break."Input schema / properties / citations / items / properties / firstPage / patternAdded value: +"^[^|\\r\\n]*$"Input schema / properties / citations / items / properties / journal / descriptionPrevious value: -"Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\")"New value: +"Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break."Input schema / properties / citations / items / properties / journal / patternAdded value: +"^[^|\\r\\n]*$"Input schema / properties / citations / items / properties / key / descriptionPrevious value: -"Arbitrary label to track this citation in results. Auto-assigned if omitted."New value: +"Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here."Input schema / properties / citations / items / properties / volume / descriptionPrevious value: -"Volume number"New value: +"Volume number. Cannot contain a pipe (\"|\") or a line break."Input schema / properties / citations / items / properties / volume / patternAdded value: +"^[^|\\r\\n]*$"Input schema / properties / citations / items / properties / year / descriptionPrevious value: -"Publication year (e.g., \"1991\")"New value: +"Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break."Input schema / properties / citations / items / properties / year / patternAdded value: +"^[^|\\r\\n]*$"pubmed_search_articles6 fields changedOutput schema / properties / summaries / items / properties / authors / descriptionPrevious value: -"Formatted author string"New value: +"Formatted author string — the first three of the record's own authors, then \"et al.\". On an NCBI Bookshelf chapter these are the chapter's authors; the book's editors are reported separately in `editors`."Output schema / properties / summaries / items / properties / bookTitleAdded value: +{
+ "description": "Title of the book an NCBI Bookshelf record belongs to, e.g. \"GeneReviews(®)\". Present instead of `source` on a book record; absent on a journal article.",
+ "type": "string"
+}Output schema / properties / summaries / items / properties / docTypeAdded value: +{
+ "description": "What PubMed classifies this record as: \"chapter\" or \"book\" for an NCBI Bookshelf record, \"citation\" for an ordinary journal article. Absent when PubMed supplies none.",
+ "type": "string"
+}Output schema / properties / summaries / items / properties / editorsAdded value: +{
+ "description": "Editors of the containing book, kept out of `authors` so they cannot displace the record's own authors. Absent on a journal article and on a book that credits no editors.",
+ "items": {
+ "description": "One editor, \"Surname Initials\" as ESummary renders it",
+ "type": "string"
+ },
+ "type": "array"
+}Output schema / properties / summaries / items / properties / publisherNameAdded value: +{
+ "description": "Publisher of the book an NCBI Bookshelf record belongs to. Present only on a book record; absent on a journal article.",
+ "type": "string"
+}Output schema / properties / summaries / items / properties / source / descriptionPrevious value: -"Journal source"New value: +"Journal the article appeared in. Absent on an NCBI Bookshelf record, which has no journal — its venue is in `bookTitle` and `publisherName` instead, and `docType` says which kind of record it is."pubmed_fetch_fulltext11 fields changedInput schema / properties / includeAssetsAdded value: +{
+ "default": true,
+ "description": "Include the article's figures and supplementary material — `assets[]`, each with its label, caption, enclosing section and deposit pointer. On by default because it is cheaper than tables: a median asset-bearing article grows about 10%, and the body prose already refers to these by label. Set false to omit them, which also removes the `[Figure: …]` / `[Supplementary: …]` markers from the section text, since without the array they point at nothing. Prose-shaped blocks — lists, definition lists, block quotes, boxed text, preformatted blocks, displayed formulae — are section text rather than assets and this switch never affects them. Applies to `source=pmc` results only.",
+ "type": "boolean"
+}Input schema / properties / maxCharacters / descriptionPrevious value: -"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text plus table label, caption, cell and footnote text, or the `source=unpaywall` `content` body; titles, abstracts, identifiers, and references are never counted or shortened. The counted unit is that text alone — the Markdown grid `content[]` renders around the cells (pipes, padding, the divider row, headings) is scaffolding this budget does not measure, so a table renders longer than it costs here. Sections are served first and tables spend what is left, in document order — admission stops at the first table that does not fit, and every table from there on is dropped whole rather than cut mid-row, counted in `truncation.omittedTables` and named in `truncation.articles[].omittedTableNames`. Applied after `sections`, `maxSections`, `includeReferences`, and `includeTables`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body."New value: +"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text — which carries the inline blocks the parser renders in place, such as lists, definition lists, block quotes, boxed text, preformatted blocks and displayed formulae — plus table label, caption, cell and footnote text and asset label, caption and `href` text; or the `source=unpaywall` `content` body. Titles, abstracts, identifiers, and references are never counted or shortened. The counted unit is that text alone — the Markdown grid `content[]` renders around the cells (pipes, padding, the divider row, headings) is scaffolding this budget does not measure, so a table renders longer than it costs here. Sections are served first, then tables, then assets, each spending what is left, in document order — admission stops at the first entry that does not fit, and every entry from there on is dropped whole rather than cut mid-row or returned with a shortened caption, counted in `truncation.omittedTables` / `truncation.omittedAssets` and named in `truncation.articles[].omittedTableNames` / `omittedAssetNames`. Applied after `sections`, `maxSections`, `includeReferences`, `includeTables`, and `includeAssets`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body."Input schema / properties / sections / descriptionPrevious value: -"Filter to specific sections by title (e.g. [\"Introduction\", \"Methods\", \"Results\", \"Discussion\"]). A term matches a section or subsection title at any nesting depth, case-insensitively, as a substring — \"resul\" matches \"Results\". A section whose own title matches is returned whole; one kept only because a nested subsection matched keeps its heading as a breadcrumb, with its own text cleared and only the matching branch beneath it. Tables narrow with the filter: one whose section did not survive, or that names no section, is dropped. Applies to `source=pmc` results only."New value: +"Filter to specific sections by title (e.g. [\"Introduction\", \"Methods\", \"Results\", \"Discussion\"]). A term matches a section or subsection title at any nesting depth, case-insensitively, as a substring — \"resul\" matches \"Results\". A section whose own title matches is returned whole; one kept only because a nested subsection matched keeps its heading as a breadcrumb, with its own text cleared and only the matching branch beneath it. Tables and assets narrow with the filter: one whose section did not survive, or that names no section, is dropped. Applies to `source=pmc` results only."Output schema / properties / articles / items / oneOfPrevious value: -[
- {
- "additionalProperties": false,
- "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
- "properties": {
- "abstract": {
- "description": "Abstract",
- "type": "string"
- },
- "affiliations": {
- "description": "Author affiliations",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "articleType": {
- "description": "Article type",
- "type": "string"
- },
- "authors": {
- "description": "Authors",
- "items": {
- "additionalProperties": false,
- "description": "Author entry",
- "properties": {
- "collectiveName": {
- "description": "Group name",
- "type": "string"
- },
- "givenNames": {
- "description": "Given names",
- "type": "string"
- },
- "lastName": {
- "description": "Last name",
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "doi": {
- "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
- "type": "string"
- },
- "epmcId": {
- "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
- "type": "string"
- },
- "epmcSource": {
- "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
- "type": "string"
- },
- "journal": {
- "additionalProperties": false,
- "description": "Journal information",
- "properties": {
- "issn": {
- "description": "ISSN",
- "type": "string"
- },
- "issue": {
- "description": "Issue number",
- "type": "string"
- },
- "pages": {
- "description": "Page range",
- "type": "string"
- },
- "title": {
- "description": "Journal title",
- "type": "string"
- },
- "volume": {
- "description": "Volume number",
- "type": "string"
- }
- },
- "type": "object"
- },
- "keywords": {
- "description": "Keywords",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "pmcId": {
- "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
- "type": "string"
- },
- "pmcUrl": {
- "description": "PMC URL — derived from `pmcId` when present",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID",
- "type": "string"
- },
- "publicationDate": {
- "additionalProperties": false,
- "description": "Publication date",
- "properties": {
- "day": {
- "description": "Publication day",
- "type": "string"
- },
- "month": {
- "description": "Publication month",
- "type": "string"
- },
- "year": {
- "description": "Publication year",
- "type": "string"
- }
- },
- "type": "object"
- },
- "pubmedUrl": {
- "description": "PubMed URL",
- "type": "string"
- },
- "references": {
- "description": "Reference list",
- "items": {
- "additionalProperties": false,
- "description": "Reference entry",
- "properties": {
- "citation": {
- "description": "Citation text",
- "type": "string"
- },
- "id": {
- "description": "Reference ID",
- "type": "string"
- },
- "label": {
- "description": "Reference label",
- "type": "string"
- }
- },
- "required": [
- "citation"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "sections": {
- "description": "Article body sections",
- "items": {
- "additionalProperties": false,
- "description": "Article body section",
- "properties": {
- "label": {
- "description": "Section label",
- "type": "string"
- },
- "subsections": {
- "description": "Nested subsections",
- "items": {
- "additionalProperties": false,
- "description": "Article subsection",
- "properties": {
- "label": {
- "description": "Subsection label",
- "type": "string"
- },
- "text": {
- "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
- "type": "string"
- },
- "title": {
- "description": "Subsection heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "text": {
- "description": "Section body text",
- "type": "string"
- },
- "title": {
- "description": "Section heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "source": {
- "const": "pmc",
- "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
- "type": "string"
- },
- "tables": {
- "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
- "items": {
- "additionalProperties": false,
- "description": "One table from the article, with its cells, caption, and owning section",
- "properties": {
- "caption": {
- "description": "Caption text, with the label excluded",
- "type": "string"
- },
- "footnotes": {
- "description": "`<table-wrap-foot>` text, flattened to one string",
- "type": "string"
- },
- "headerRowCount": {
- "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
- "type": "number"
- },
- "id": {
- "description": "JATS `id` attribute — the target body-text cross-references point at",
- "type": "string"
- },
- "label": {
- "description": "Table label as printed, e.g. `TABLE 1`",
- "type": "string"
- },
- "rows": {
- "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. Empty when `unextractableReason` is set.",
- "items": {
- "description": "One row, as cell text by grid column",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "type": "array"
- },
- "sectionTitle": {
- "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
- "type": "string"
- },
- "unextractableReason": {
- "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
- "enum": [
- "cals-tgroup",
- "graphic-only",
- "no-rows"
- ],
- "type": "string"
- }
- },
- "required": [
- "headerRowCount",
- "rows"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "title": {
- "description": "Article title",
- "type": "string"
- },
- "viaSource": {
- "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
- "enum": [
- "pmc",
- "europepmc"
- ],
- "type": "string"
- }
- },
- "required": [
- "source",
- "viaSource",
- "sections"
- ],
- "type": "object"
- },
- {
- "additionalProperties": false,
- "description": "Best-effort full text from an open-access copy",
- "properties": {
- "content": {
- "description": "Full article text — Markdown or plain text per `contentFormat`",
- "type": "string"
- },
- "contentFormat": {
- "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
- "enum": [
- "html-markdown",
- "pdf-text"
- ],
- "type": "string"
- },
- "doi": {
- "description": "DOI used to locate the open-access copy",
- "type": "string"
- },
- "hostType": {
- "description": "`publisher` or `repository` — where the OA copy is hosted",
- "type": "string"
- },
- "license": {
- "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
- "type": "string"
- },
- "pmcId": {
- "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
- "type": "string"
- },
- "pubmedUrl": {
- "description": "PubMed URL — present when `pmid` is set",
- "type": "string"
- },
- "source": {
- "const": "unpaywall",
- "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
- "type": "string"
- },
- "sourceUrl": {
- "description": "URL the content was fetched from",
- "type": "string"
- },
- "title": {
- "description": "Detected article title when present",
- "type": "string"
- },
- "totalPages": {
- "description": "Page count reported by the PDF extractor; absent for HTML",
- "type": "number"
- },
- "version": {
- "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
- "type": "string"
- },
- "viaSource": {
- "const": "unpaywall",
- "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
- "type": "string"
- },
- "wordCount": {
- "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
- "type": "number"
- }
- },
- "required": [
- "source",
- "viaSource",
- "contentFormat",
- "doi",
- "sourceUrl",
- "content"
- ],
- "type": "object"
- }
-]New value: +[
+ {
+ "additionalProperties": false,
+ "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
+ "properties": {
+ "abstract": {
+ "description": "Abstract",
+ "type": "string"
+ },
+ "affiliations": {
+ "description": "Author affiliations",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "articleType": {
+ "description": "Article type",
+ "type": "string"
+ },
+ "assets": {
+ "description": "Every `<fig>` and `<supplementary-material>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Each one lifted from the body leaves a `[Figure: <label>]` or `[Supplementary: <label>]` marker at its position in the section text, so reading order survives the lift. Absent when the article deposits none, when `includeAssets` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One figure or supplementary-material item, with its caption, pointer, and section",
+ "properties": {
+ "assetType": {
+ "description": "Which captioned element this came from — `figure` for a `<fig>`, `supplementary-material` for a `<supplementary-material>` deposit",
+ "enum": [
+ "figure",
+ "supplementary-material"
+ ],
+ "type": "string"
+ },
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "href": {
+ "description": "The `<graphic>`/`<media>` `@xlink:href` exactly as deposited — a pointer into the PMC deposit (`MOL2-20-1253-g001.jpg`), not a fetchable URL. No absolute form of it resolves; read the rendered article at `pmcUrl` instead. Absent when the deposit names no file.",
+ "type": "string"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Display label as printed, e.g. `Fig. 1`",
+ "type": "string"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost section enclosing the asset, wherever that section sits — body, `<back>` matter, or an appendix all count. Absent for an asset inside no section at all, such as a `<floats-group>` deposit.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "assetType"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "authors": {
+ "description": "Authors",
+ "items": {
+ "additionalProperties": false,
+ "description": "Author entry",
+ "properties": {
+ "collectiveName": {
+ "description": "Group name",
+ "type": "string"
+ },
+ "givenNames": {
+ "description": "Given names",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Last name",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "doi": {
+ "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
+ "type": "string"
+ },
+ "epmcId": {
+ "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
+ "type": "string"
+ },
+ "epmcSource": {
+ "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
+ "type": "string"
+ },
+ "journal": {
+ "additionalProperties": false,
+ "description": "Journal information",
+ "properties": {
+ "issn": {
+ "description": "ISSN",
+ "type": "string"
+ },
+ "issue": {
+ "description": "Issue number",
+ "type": "string"
+ },
+ "pages": {
+ "description": "Page range",
+ "type": "string"
+ },
+ "title": {
+ "description": "Journal title",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "keywords": {
+ "description": "Keywords",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "pmcId": {
+ "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
+ "type": "string"
+ },
+ "pmcUrl": {
+ "description": "PMC URL — derived from `pmcId` when present",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID",
+ "type": "string"
+ },
+ "publicationDate": {
+ "additionalProperties": false,
+ "description": "Publication date",
+ "properties": {
+ "day": {
+ "description": "Publication day",
+ "type": "string"
+ },
+ "month": {
+ "description": "Publication month",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL",
+ "type": "string"
+ },
+ "references": {
+ "description": "Reference list",
+ "items": {
+ "additionalProperties": false,
+ "description": "Reference entry",
+ "properties": {
+ "citation": {
+ "description": "Citation text",
+ "type": "string"
+ },
+ "id": {
+ "description": "Reference ID",
+ "type": "string"
+ },
+ "label": {
+ "description": "Reference label",
+ "type": "string"
+ }
+ },
+ "required": [
+ "citation"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "sections": {
+ "description": "Article body sections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article body section",
+ "properties": {
+ "label": {
+ "description": "Section label",
+ "type": "string"
+ },
+ "subsections": {
+ "description": "Nested subsections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article subsection",
+ "properties": {
+ "label": {
+ "description": "Subsection label",
+ "type": "string"
+ },
+ "text": {
+ "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
+ "type": "string"
+ },
+ "title": {
+ "description": "Subsection heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "text": {
+ "description": "Section body text",
+ "type": "string"
+ },
+ "title": {
+ "description": "Section heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "source": {
+ "const": "pmc",
+ "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
+ "type": "string"
+ },
+ "tables": {
+ "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One table from the article, with its cells, caption, and owning section",
+ "properties": {
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "footnotes": {
+ "description": "`<table-wrap-foot>` text, flattened to one string",
+ "type": "string"
+ },
+ "headerRowCount": {
+ "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
+ "type": "number"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Table label as printed, e.g. `TABLE 1`",
+ "type": "string"
+ },
+ "rows": {
+ "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. Empty when `unextractableReason` is set.",
+ "items": {
+ "description": "One row, as cell text by grid column",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "type": "array"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
+ "type": "string"
+ },
+ "unextractableReason": {
+ "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
+ "enum": [
+ "cals-tgroup",
+ "graphic-only",
+ "no-rows"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "headerRowCount",
+ "rows"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "title": {
+ "description": "Article title",
+ "type": "string"
+ },
+ "viaSource": {
+ "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
+ "enum": [
+ "pmc",
+ "europepmc"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "sections"
+ ],
+ "type": "object"
+ },
+ {
+ "additionalProperties": false,
+ "description": "Best-effort full text from an open-access copy",
+ "properties": {
+ "content": {
+ "description": "Full article text — Markdown or plain text per `contentFormat`",
+ "type": "string"
+ },
+ "contentFormat": {
+ "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
+ "enum": [
+ "html-markdown",
+ "pdf-text"
+ ],
+ "type": "string"
+ },
+ "doi": {
+ "description": "DOI used to locate the open-access copy",
+ "type": "string"
+ },
+ "hostType": {
+ "description": "`publisher` or `repository` — where the OA copy is hosted",
+ "type": "string"
+ },
+ "license": {
+ "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
+ "type": "string"
+ },
+ "pmcId": {
+ "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
+ "type": "string"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL — present when `pmid` is set",
+ "type": "string"
+ },
+ "source": {
+ "const": "unpaywall",
+ "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
+ "type": "string"
+ },
+ "sourceUrl": {
+ "description": "URL the content was fetched from",
+ "type": "string"
+ },
+ "title": {
+ "description": "Detected article title when present",
+ "type": "string"
+ },
+ "totalPages": {
+ "description": "Page count reported by the PDF extractor; absent for HTML",
+ "type": "number"
+ },
+ "version": {
+ "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
+ "type": "string"
+ },
+ "viaSource": {
+ "const": "unpaywall",
+ "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
+ "type": "string"
+ },
+ "wordCount": {
+ "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
+ "type": "number"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "contentFormat",
+ "doi",
+ "sourceUrl",
+ "content"
+ ],
+ "type": "object"
+ }
+]Output schema / properties / truncation / properties / articles / items / properties / omittedAssetNamesAdded value: +{
+ "description": "The dropped assets by name, in document order — each asset's label, else its `id`, else `asset <n>` for its position in the article. Contiguous for the same reason `omittedTableNames` is: admission stops at the first asset that did not fit rather than skipping ahead to a smaller one. Absent when none were dropped.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+}Output schema / properties / truncation / properties / articles / items / properties / omittedAssetsAdded value: +{
+ "description": "Figures and supplementary items this article dropped whole because the budget left no room once sections and tables were served. An asset is never returned with a truncated caption, so it is either returned complete or counted here. Absent when none were dropped.",
+ "type": "number"
+}Output schema / properties / truncation / properties / omittedAssetsAdded value: +{
+ "description": "Figures and supplementary items dropped whole across every budgeted article, because the budget left no room once body sections and tables were served. Absent when none were dropped. Re-request the affected articles with a higher `maxCharacters`, or with `sections` narrowed, to receive them.",
+ "type": "number"
+}Output schema / properties / unavailable / items / properties / reason / descriptionPrevious value: -"Why no full text was returned — the most specific signal any tier that answered reported. not-found: upstream returned no record for this ID. no-pmc-fallback-disabled: every tier was skipped (`triedTiers` is all `not-attempted`) — typically because EPMC (`EUROPEPMC_ENABLED`) and Unpaywall (`UNPAYWALL_EMAIL`) are not configured. no-epmc-fulltext: EPMC indexed the record but publishes no fullTextXML. no-body: the record was retrieved but carries front matter and abstract only, with no body sections — use `pubmed_fetch_articles` for the metadata. no-doi: no DOI to query Unpaywall. no-oa: Unpaywall has no OA copy. fetch-failed: download failed. parse-failed: extraction empty. service-error: upstream server failure (threw, timed out, or returned malformed data). A reason never means the chain ran to completion — read `unqueriedTiers` for that."New value: +"Why no full text was returned — the most specific signal any tier that answered reported. not-found: upstream returned no record for this ID. no-pmc-fallback-disabled: every tier was skipped (`triedTiers` is all `not-attempted`) — typically because EPMC (`EUROPEPMC_ENABLED`) and Unpaywall (`UNPAYWALL_EMAIL`) are not configured. no-epmc-fulltext: EPMC indexed the record but publishes no fullTextXML. no-body: the record was retrieved but carries front matter and abstract only, with no body sections — use `pubmed_fetch_articles` for the metadata. no-doi: the DOI lookup ran and this record has none, so Unpaywall could not be queried. doi-lookup-failed: the DOI lookup itself errored, so whether a DOI exists is unknown and Unpaywall was never reached — retry the request; unlike no-doi this is a transient failure, not a settled answer. no-oa: Unpaywall has no OA copy. fetch-failed: download failed. parse-failed: extraction empty. service-error: upstream server failure (threw, timed out, or returned malformed data). A reason never means the chain ran to completion — read `unqueriedTiers` for that."Output schema / properties / unavailable / items / properties / reason / enumPrevious value: -[
- "not-found",
- "no-pmc-fallback-disabled",
- "no-epmc-fulltext",
- "no-body",
- "no-doi",
- "no-oa",
- "fetch-failed",
- "parse-failed",
- "service-error"
-]New value: +[
+ "not-found",
+ "no-pmc-fallback-disabled",
+ "no-epmc-fulltext",
+ "no-body",
+ "no-doi",
+ "doi-lookup-failed",
+ "no-oa",
+ "fetch-failed",
+ "parse-failed",
+ "service-error"
+]Output schema / properties / unavailable / items / properties / triedTiers / items / properties / outcome / descriptionPrevious value: -"Per-tier outcome. not-attempted: tier was skipped. miss: tier returned no record. no-fulltext: EPMC indexed the record but publishes no fullTextXML. no-body: the tier returned a record with front matter and abstract but no body sections, so the chain continued. no-doi: no DOI to query Unpaywall. no-oa: Unpaywall reports no open-access copy. fetch-failed: OA copy download failed. parse-failed: extraction produced empty content. service-error: tier service threw."New value: +"Per-tier outcome. not-attempted: tier was skipped. miss: tier returned no record. no-fulltext: EPMC indexed the record but publishes no fullTextXML. no-body: the tier returned a record with front matter and abstract but no body sections, so the chain continued. no-doi: the DOI lookup ran and this record has none, so Unpaywall could not be queried. doi-lookup-failed: the DOI lookup itself errored, so whether a DOI exists is unknown and Unpaywall was never reached — retry the request. no-oa: Unpaywall reports no open-access copy. fetch-failed: OA copy download failed. parse-failed: extraction produced empty content. service-error: tier service threw."Output schema / properties / unavailable / items / properties / triedTiers / items / properties / outcome / enumPrevious value: -[
- "not-attempted",
- "miss",
- "no-fulltext",
- "no-body",
- "no-doi",
- "no-oa",
- "fetch-failed",
- "parse-failed",
- "service-error"
-]New value: +[
+ "not-attempted",
+ "miss",
+ "no-fulltext",
+ "no-body",
+ "no-doi",
+ "doi-lookup-failed",
+ "no-oa",
+ "fetch-failed",
+ "parse-failed",
+ "service-error"
+]pubmed_find_related3 fields changedOutput schema / properties / coverageFailuresAdded value: +{
+ "description": "Reference-coverage fallbacks that failed instead of answering, so the reference set is unverified rather than confirmed absent. Absent when every provider consulted answered.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One coverage provider that could not be checked",
+ "properties": {
+ "provider": {
+ "description": "Reference-coverage provider that failed",
+ "enum": [
+ "europepmc",
+ "openalex"
+ ],
+ "type": "string"
+ },
+ "reason": {
+ "description": "Declared failure reason, e.g. europepmc_unreachable or provider_disabled",
+ "type": "string"
+ },
+ "retryable": {
+ "description": "Whether a retry can reach this provider",
+ "type": "boolean"
+ }
+ },
+ "required": [
+ "provider",
+ "reason",
+ "retryable"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+}Output schema / properties / notice / descriptionPrevious value: -"Guidance when results are empty, a fallback provider answered, offset overshot, or Europe PMC rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page."New value: +"Guidance when results are empty, a fallback provider answered, offset overshot, a fallback provider could not be reached, or upstream rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page."Output schema / properties / totalCount / descriptionPrevious value: -"Total related articles found before windowing. A Europe PMC total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned."New value: +"Total related articles found before windowing. A Europe PMC or OpenAlex total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned."pubmed_lookup_mesh3 fields changedInput schema / properties / query / descriptionPrevious value: -"MeSH descriptor name or free-text term to look up"New value: +"MeSH descriptor name or free-text term to look up. Must carry a term: a blank or whitespace-only value is rejected rather than searched."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "blank_query"
+]pubmed_search_articles3 fields changedInput schema / properties / query / descriptionPrevious value: -"PubMed search query (supports full NCBI syntax)"New value: +"PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup is stripped is rejected rather than sent to PubMed as an empty term."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "blank_query"
+]pubmed_spell_check3 fields changedInput schema / properties / query / descriptionPrevious value: -"PubMed search query to spell-check"New value: +"PubMed search query to spell-check. Must carry a term: a blank or whitespace-only value is rejected rather than sent to ESpell."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `blank_query`: The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "blank_query"
+]pubmed_fetch_fulltext8 fields changedInput schema / properties / includeTablesAdded value: +{
+ "default": true,
+ "description": "Include the article's tables — cells, captions, labels and footnotes. On by default because a dropped table takes its numbers with it. Table-dense articles pay for it: rendered tables typically add 12–17% to an article record and can more than double it. Set false to omit them, or cap the cost with `maxCharacters`, which drops tables it cannot fit whole. Applies to `source=pmc` results only.",
+ "type": "boolean"
+}Input schema / properties / maxCharacters / descriptionPrevious value: -"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text, or the `source=unpaywall` `content` body; titles, abstracts, identifiers, and references are never counted or shortened. Applied after `sections`, `maxSections`, and `includeReferences`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body."New value: +"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text plus table label, caption, cell and footnote text, or the `source=unpaywall` `content` body; titles, abstracts, identifiers, and references are never counted or shortened. The counted unit is that text alone — the Markdown grid `content[]` renders around the cells (pipes, padding, the divider row, headings) is scaffolding this budget does not measure, so a table renders longer than it costs here. Sections are served first and tables spend what is left, in document order — admission stops at the first table that does not fit, and every table from there on is dropped whole rather than cut mid-row, counted in `truncation.omittedTables` and named in `truncation.articles[].omittedTableNames`. Applied after `sections`, `maxSections`, `includeReferences`, and `includeTables`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body."Input schema / properties / sections / descriptionPrevious value: -"Filter to specific sections by title, case-insensitive (e.g. [\"Introduction\", \"Methods\", \"Results\", \"Discussion\"]). Applies to `source=pmc` results only."New value: +"Filter to specific sections by title (e.g. [\"Introduction\", \"Methods\", \"Results\", \"Discussion\"]). A term matches a section or subsection title at any nesting depth, case-insensitively, as a substring — \"resul\" matches \"Results\". A section whose own title matches is returned whole; one kept only because a nested subsection matched keeps its heading as a breadcrumb, with its own text cleared and only the matching branch beneath it. Tables narrow with the filter: one whose section did not survive, or that names no section, is dropped. Applies to `source=pmc` results only."Output schema / properties / articles / items / oneOfPrevious value: -[
- {
- "additionalProperties": false,
- "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
- "properties": {
- "abstract": {
- "description": "Abstract",
- "type": "string"
- },
- "affiliations": {
- "description": "Author affiliations",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "articleType": {
- "description": "Article type",
- "type": "string"
- },
- "authors": {
- "description": "Authors",
- "items": {
- "additionalProperties": false,
- "description": "Author entry",
- "properties": {
- "collectiveName": {
- "description": "Group name",
- "type": "string"
- },
- "givenNames": {
- "description": "Given names",
- "type": "string"
- },
- "lastName": {
- "description": "Last name",
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "doi": {
- "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
- "type": "string"
- },
- "epmcId": {
- "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
- "type": "string"
- },
- "epmcSource": {
- "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
- "type": "string"
- },
- "journal": {
- "additionalProperties": false,
- "description": "Journal information",
- "properties": {
- "issn": {
- "description": "ISSN",
- "type": "string"
- },
- "issue": {
- "description": "Issue number",
- "type": "string"
- },
- "pages": {
- "description": "Page range",
- "type": "string"
- },
- "title": {
- "description": "Journal title",
- "type": "string"
- },
- "volume": {
- "description": "Volume number",
- "type": "string"
- }
- },
- "type": "object"
- },
- "keywords": {
- "description": "Keywords",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "pmcId": {
- "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
- "type": "string"
- },
- "pmcUrl": {
- "description": "PMC URL — derived from `pmcId` when present",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID",
- "type": "string"
- },
- "publicationDate": {
- "additionalProperties": false,
- "description": "Publication date",
- "properties": {
- "day": {
- "description": "Publication day",
- "type": "string"
- },
- "month": {
- "description": "Publication month",
- "type": "string"
- },
- "year": {
- "description": "Publication year",
- "type": "string"
- }
- },
- "type": "object"
- },
- "pubmedUrl": {
- "description": "PubMed URL",
- "type": "string"
- },
- "references": {
- "description": "Reference list",
- "items": {
- "additionalProperties": false,
- "description": "Reference entry",
- "properties": {
- "citation": {
- "description": "Citation text",
- "type": "string"
- },
- "id": {
- "description": "Reference ID",
- "type": "string"
- },
- "label": {
- "description": "Reference label",
- "type": "string"
- }
- },
- "required": [
- "citation"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "sections": {
- "description": "Article body sections",
- "items": {
- "additionalProperties": false,
- "description": "Article body section",
- "properties": {
- "label": {
- "description": "Section label",
- "type": "string"
- },
- "subsections": {
- "description": "Nested subsections",
- "items": {
- "additionalProperties": false,
- "description": "Article subsection",
- "properties": {
- "label": {
- "description": "Subsection label",
- "type": "string"
- },
- "text": {
- "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
- "type": "string"
- },
- "title": {
- "description": "Subsection heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "text": {
- "description": "Section body text",
- "type": "string"
- },
- "title": {
- "description": "Section heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "source": {
- "const": "pmc",
- "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
- "type": "string"
- },
- "title": {
- "description": "Article title",
- "type": "string"
- },
- "viaSource": {
- "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
- "enum": [
- "pmc",
- "europepmc"
- ],
- "type": "string"
- }
- },
- "required": [
- "source",
- "viaSource",
- "sections"
- ],
- "type": "object"
- },
- {
- "additionalProperties": false,
- "description": "Best-effort full text from an open-access copy",
- "properties": {
- "content": {
- "description": "Full article text — Markdown or plain text per `contentFormat`",
- "type": "string"
- },
- "contentFormat": {
- "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
- "enum": [
- "html-markdown",
- "pdf-text"
- ],
- "type": "string"
- },
- "doi": {
- "description": "DOI used to locate the open-access copy",
- "type": "string"
- },
- "hostType": {
- "description": "`publisher` or `repository` — where the OA copy is hosted",
- "type": "string"
- },
- "license": {
- "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
- "type": "string"
- },
- "pmcId": {
- "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
- "type": "string"
- },
- "pubmedUrl": {
- "description": "PubMed URL — present when `pmid` is set",
- "type": "string"
- },
- "source": {
- "const": "unpaywall",
- "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
- "type": "string"
- },
- "sourceUrl": {
- "description": "URL the content was fetched from",
- "type": "string"
- },
- "title": {
- "description": "Detected article title when present",
- "type": "string"
- },
- "totalPages": {
- "description": "Page count reported by the PDF extractor; absent for HTML",
- "type": "number"
- },
- "version": {
- "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
- "type": "string"
- },
- "viaSource": {
- "const": "unpaywall",
- "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
- "type": "string"
- },
- "wordCount": {
- "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
- "type": "number"
- }
- },
- "required": [
- "source",
- "viaSource",
- "contentFormat",
- "doi",
- "sourceUrl",
- "content"
- ],
- "type": "object"
- }
-]New value: +[
+ {
+ "additionalProperties": false,
+ "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
+ "properties": {
+ "abstract": {
+ "description": "Abstract",
+ "type": "string"
+ },
+ "affiliations": {
+ "description": "Author affiliations",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "articleType": {
+ "description": "Article type",
+ "type": "string"
+ },
+ "authors": {
+ "description": "Authors",
+ "items": {
+ "additionalProperties": false,
+ "description": "Author entry",
+ "properties": {
+ "collectiveName": {
+ "description": "Group name",
+ "type": "string"
+ },
+ "givenNames": {
+ "description": "Given names",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Last name",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "doi": {
+ "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
+ "type": "string"
+ },
+ "epmcId": {
+ "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
+ "type": "string"
+ },
+ "epmcSource": {
+ "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
+ "type": "string"
+ },
+ "journal": {
+ "additionalProperties": false,
+ "description": "Journal information",
+ "properties": {
+ "issn": {
+ "description": "ISSN",
+ "type": "string"
+ },
+ "issue": {
+ "description": "Issue number",
+ "type": "string"
+ },
+ "pages": {
+ "description": "Page range",
+ "type": "string"
+ },
+ "title": {
+ "description": "Journal title",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "keywords": {
+ "description": "Keywords",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "pmcId": {
+ "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
+ "type": "string"
+ },
+ "pmcUrl": {
+ "description": "PMC URL — derived from `pmcId` when present",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID",
+ "type": "string"
+ },
+ "publicationDate": {
+ "additionalProperties": false,
+ "description": "Publication date",
+ "properties": {
+ "day": {
+ "description": "Publication day",
+ "type": "string"
+ },
+ "month": {
+ "description": "Publication month",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL",
+ "type": "string"
+ },
+ "references": {
+ "description": "Reference list",
+ "items": {
+ "additionalProperties": false,
+ "description": "Reference entry",
+ "properties": {
+ "citation": {
+ "description": "Citation text",
+ "type": "string"
+ },
+ "id": {
+ "description": "Reference ID",
+ "type": "string"
+ },
+ "label": {
+ "description": "Reference label",
+ "type": "string"
+ }
+ },
+ "required": [
+ "citation"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "sections": {
+ "description": "Article body sections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article body section",
+ "properties": {
+ "label": {
+ "description": "Section label",
+ "type": "string"
+ },
+ "subsections": {
+ "description": "Nested subsections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article subsection",
+ "properties": {
+ "label": {
+ "description": "Subsection label",
+ "type": "string"
+ },
+ "text": {
+ "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
+ "type": "string"
+ },
+ "title": {
+ "description": "Subsection heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "text": {
+ "description": "Section body text",
+ "type": "string"
+ },
+ "title": {
+ "description": "Section heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "source": {
+ "const": "pmc",
+ "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
+ "type": "string"
+ },
+ "tables": {
+ "description": "Every `<table-wrap>` the article carries, in document order — from the body and from `<floats-group>`, `<back>` and appendices alike. Absent when the article deposits none, when `includeTables` is false, or when a `sections` filter left none standing.",
+ "items": {
+ "additionalProperties": false,
+ "description": "One table from the article, with its cells, caption, and owning section",
+ "properties": {
+ "caption": {
+ "description": "Caption text, with the label excluded",
+ "type": "string"
+ },
+ "footnotes": {
+ "description": "`<table-wrap-foot>` text, flattened to one string",
+ "type": "string"
+ },
+ "headerRowCount": {
+ "description": "How many leading `rows` entries are header rows — a `<thead>` block, or leading rows made entirely of `<th>`. 0 when the table declares none. Several header rows stack: read one column top to bottom for its full header path.",
+ "type": "number"
+ },
+ "id": {
+ "description": "JATS `id` attribute — the target body-text cross-references point at",
+ "type": "string"
+ },
+ "label": {
+ "description": "Table label as printed, e.g. `TABLE 1`",
+ "type": "string"
+ },
+ "rows": {
+ "description": "Cell text by row, in document order, one entry per grid column. `colspan` and `rowspan` are expanded, so a cell covering several columns or rows repeats its text across each cell it covers and a well-formed table is rectangular — align on position from the left, and read a repeated value as one spanning cell rather than several measurements. Empty when `unextractableReason` is set.",
+ "items": {
+ "description": "One row, as cell text by grid column",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "type": "array"
+ },
+ "sectionTitle": {
+ "description": "Title of the innermost section enclosing the table, wherever that section sits — body, `<back>` matter, or an appendix all count, and in back matter the section name is the only positional cue there is. Absent only for a table inside no section at all, such as a `<floats-group>` deposit.",
+ "type": "string"
+ },
+ "unextractableReason": {
+ "description": "Why `rows` is empty — set only then. graphic-only: the table was deposited as an image with no underlying markup. cals-tgroup: the table uses the CALS `<tgroup>` model, which this server does not extract (0 of 283 tables in an open-access survey used it). no-rows: the markup carried no rows. The label and caption are still returned, so a table that could not be read is visible rather than silently missing.",
+ "enum": [
+ "cals-tgroup",
+ "graphic-only",
+ "no-rows"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "headerRowCount",
+ "rows"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "title": {
+ "description": "Article title",
+ "type": "string"
+ },
+ "viaSource": {
+ "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
+ "enum": [
+ "pmc",
+ "europepmc"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "sections"
+ ],
+ "type": "object"
+ },
+ {
+ "additionalProperties": false,
+ "description": "Best-effort full text from an open-access copy",
+ "properties": {
+ "content": {
+ "description": "Full article text — Markdown or plain text per `contentFormat`",
+ "type": "string"
+ },
+ "contentFormat": {
+ "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
+ "enum": [
+ "html-markdown",
+ "pdf-text"
+ ],
+ "type": "string"
+ },
+ "doi": {
+ "description": "DOI used to locate the open-access copy",
+ "type": "string"
+ },
+ "hostType": {
+ "description": "`publisher` or `repository` — where the OA copy is hosted",
+ "type": "string"
+ },
+ "license": {
+ "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
+ "type": "string"
+ },
+ "pmcId": {
+ "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
+ "type": "string"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL — present when `pmid` is set",
+ "type": "string"
+ },
+ "source": {
+ "const": "unpaywall",
+ "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
+ "type": "string"
+ },
+ "sourceUrl": {
+ "description": "URL the content was fetched from",
+ "type": "string"
+ },
+ "title": {
+ "description": "Detected article title when present",
+ "type": "string"
+ },
+ "totalPages": {
+ "description": "Page count reported by the PDF extractor; absent for HTML",
+ "type": "number"
+ },
+ "version": {
+ "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
+ "type": "string"
+ },
+ "viaSource": {
+ "const": "unpaywall",
+ "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
+ "type": "string"
+ },
+ "wordCount": {
+ "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
+ "type": "number"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "contentFormat",
+ "doi",
+ "sourceUrl",
+ "content"
+ ],
+ "type": "object"
+ }
+]Output schema / properties / notice / descriptionPrevious value: -"Optional guidance for a partial or empty body. A `sections`-filter miss names the requested terms and affected article id(s) and suggests retrying without `sections` or using broader headings. A metadata-only record names the id(s) the chain could retrieve as front matter only and points at `pubmed_fetch_articles` for the abstract. A budgeted response names the characters returned versus carried and points at `truncation`. A response-wide budget that deferred articles names the ids to re-request. Absent when none of those applies."New value: +"Optional guidance for a partial or empty body. A `sections`-filter miss names the requested terms and affected article id(s) and suggests retrying without `sections` or using broader headings. A metadata-only record names the id(s) the chain could retrieve as front matter only and points at `pubmed_fetch_articles` for the abstract. A table returned with no cell values names the affected table(s), the article each came from, and why the cells cannot be recovered. A budgeted response names the characters returned versus carried and points at `truncation`. A response-wide budget that deferred articles names the ids to re-request. Absent when none of those applies."Output schema / properties / truncation / properties / articles / items / properties / omittedTableNamesAdded value: +{
+ "description": "The dropped tables by name, in document order — each table's label, else its `id`, else `table <n>` for its position in the article. Names the tables a bare count only hints at, the way `deferred.ids` names deferred articles. Every table from the first that did not fit onward is here: admission stops at that table rather than skipping ahead to a smaller one, so these are contiguous. Absent when none were dropped.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+}Output schema / properties / truncation / properties / articles / items / properties / omittedTablesAdded value: +{
+ "description": "Tables this article dropped whole because the budget left no room for them. A table is never cut mid-row, so it is either returned complete or counted here. Absent when none were dropped.",
+ "type": "number"
+}Output schema / properties / truncation / properties / omittedTablesAdded value: +{
+ "description": "Tables dropped whole across every budgeted article, because the budget left no room once body sections were served. Absent when none were dropped. Re-request the affected articles with a higher `maxCharacters`, or with `sections` narrowed, to receive them.",
+ "type": "number"
+}pubmed_fetch_fulltext1 field changedOutput schema / properties / articles / items / oneOfPrevious value: -[
- {
- "additionalProperties": false,
- "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
- "properties": {
- "abstract": {
- "description": "Abstract",
- "type": "string"
- },
- "affiliations": {
- "description": "Author affiliations",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "articleType": {
- "description": "Article type",
- "type": "string"
- },
- "authors": {
- "description": "Authors",
- "items": {
- "additionalProperties": false,
- "description": "Author entry",
- "properties": {
- "collectiveName": {
- "description": "Group name",
- "type": "string"
- },
- "givenNames": {
- "description": "Given names",
- "type": "string"
- },
- "lastName": {
- "description": "Last name",
- "type": "string"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "doi": {
- "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
- "type": "string"
- },
- "epmcId": {
- "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
- "type": "string"
- },
- "epmcSource": {
- "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
- "type": "string"
- },
- "journal": {
- "additionalProperties": false,
- "description": "Journal information",
- "properties": {
- "issn": {
- "description": "ISSN",
- "type": "string"
- },
- "issue": {
- "description": "Issue number",
- "type": "string"
- },
- "pages": {
- "description": "Page range",
- "type": "string"
- },
- "title": {
- "description": "Journal title",
- "type": "string"
- },
- "volume": {
- "description": "Volume number",
- "type": "string"
- }
- },
- "type": "object"
- },
- "keywords": {
- "description": "Keywords",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "pmcId": {
- "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
- "type": "string"
- },
- "pmcUrl": {
- "description": "PMC URL — derived from `pmcId` when present",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID",
- "type": "string"
- },
- "publicationDate": {
- "additionalProperties": false,
- "description": "Publication date",
- "properties": {
- "day": {
- "description": "Publication day",
- "type": "string"
- },
- "month": {
- "description": "Publication month",
- "type": "string"
- },
- "year": {
- "description": "Publication year",
- "type": "string"
- }
- },
- "type": "object"
- },
- "pubmedUrl": {
- "description": "PubMed URL",
- "type": "string"
- },
- "references": {
- "description": "Reference list",
- "items": {
- "additionalProperties": false,
- "description": "Reference entry",
- "properties": {
- "citation": {
- "description": "Citation text",
- "type": "string"
- },
- "id": {
- "description": "Reference ID",
- "type": "string"
- },
- "label": {
- "description": "Reference label",
- "type": "string"
- }
- },
- "required": [
- "citation"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "sections": {
- "description": "Article body sections",
- "items": {
- "additionalProperties": false,
- "description": "Article body section",
- "properties": {
- "label": {
- "description": "Section label",
- "type": "string"
- },
- "subsections": {
- "description": "Nested subsections",
- "items": {
- "additionalProperties": false,
- "description": "Article subsection",
- "properties": {
- "label": {
- "description": "Subsection label",
- "type": "string"
- },
- "text": {
- "description": "Subsection body text",
- "type": "string"
- },
- "title": {
- "description": "Subsection heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "text": {
- "description": "Section body text",
- "type": "string"
- },
- "title": {
- "description": "Section heading",
- "type": "string"
- }
- },
- "required": [
- "text"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "source": {
- "const": "pmc",
- "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
- "type": "string"
- },
- "title": {
- "description": "Article title",
- "type": "string"
- },
- "viaSource": {
- "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
- "enum": [
- "pmc",
- "europepmc"
- ],
- "type": "string"
- }
- },
- "required": [
- "source",
- "viaSource",
- "sections"
- ],
- "type": "object"
- },
- {
- "additionalProperties": false,
- "description": "Best-effort full text from an open-access copy",
- "properties": {
- "content": {
- "description": "Full article text — Markdown or plain text per `contentFormat`",
- "type": "string"
- },
- "contentFormat": {
- "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
- "enum": [
- "html-markdown",
- "pdf-text"
- ],
- "type": "string"
- },
- "doi": {
- "description": "DOI used to locate the open-access copy",
- "type": "string"
- },
- "hostType": {
- "description": "`publisher` or `repository` — where the OA copy is hosted",
- "type": "string"
- },
- "license": {
- "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
- "type": "string"
- },
- "pmcId": {
- "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
- "type": "string"
- },
- "pmid": {
- "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
- "type": "string"
- },
- "pubmedUrl": {
- "description": "PubMed URL — present when `pmid` is set",
- "type": "string"
- },
- "source": {
- "const": "unpaywall",
- "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
- "type": "string"
- },
- "sourceUrl": {
- "description": "URL the content was fetched from",
- "type": "string"
- },
- "title": {
- "description": "Detected article title when present",
- "type": "string"
- },
- "totalPages": {
- "description": "Page count reported by the PDF extractor; absent for HTML",
- "type": "number"
- },
- "version": {
- "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
- "type": "string"
- },
- "viaSource": {
- "const": "unpaywall",
- "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
- "type": "string"
- },
- "wordCount": {
- "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
- "type": "number"
- }
- },
- "required": [
- "source",
- "viaSource",
- "contentFormat",
- "doi",
- "sourceUrl",
- "content"
- ],
- "type": "object"
- }
-]New value: +[
+ {
+ "additionalProperties": false,
+ "description": "Structured JATS full-text article. `viaSource` records whether the JATS came from NCBI PMC or Europe PMC.",
+ "properties": {
+ "abstract": {
+ "description": "Abstract",
+ "type": "string"
+ },
+ "affiliations": {
+ "description": "Author affiliations",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "articleType": {
+ "description": "Article type",
+ "type": "string"
+ },
+ "authors": {
+ "description": "Authors",
+ "items": {
+ "additionalProperties": false,
+ "description": "Author entry",
+ "properties": {
+ "collectiveName": {
+ "description": "Group name",
+ "type": "string"
+ },
+ "givenNames": {
+ "description": "Given names",
+ "type": "string"
+ },
+ "lastName": {
+ "description": "Last name",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "doi": {
+ "description": "DOI, cased as the tier that served this record reports it (NCBI PMC, Europe PMC, or Unpaywall). DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ between tiers and from other tools — compare case-insensitively.",
+ "type": "string"
+ },
+ "epmcId": {
+ "description": "Europe PMC record id — present when `viaSource` is `europepmc`",
+ "type": "string"
+ },
+ "epmcSource": {
+ "description": "Europe PMC source code when `viaSource` is `europepmc`. Common values: `MED` (PubMed-derived), `PMC` (PMC counterpart), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola), plus less common codes (`CTX`, `CBA`, `ETH`, `HIR`). Treat as opaque — EPMC may introduce new codes.",
+ "type": "string"
+ },
+ "journal": {
+ "additionalProperties": false,
+ "description": "Journal information",
+ "properties": {
+ "issn": {
+ "description": "ISSN",
+ "type": "string"
+ },
+ "issue": {
+ "description": "Issue number",
+ "type": "string"
+ },
+ "pages": {
+ "description": "Page range",
+ "type": "string"
+ },
+ "title": {
+ "description": "Journal title",
+ "type": "string"
+ },
+ "volume": {
+ "description": "Volume number",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "keywords": {
+ "description": "Keywords",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "pmcId": {
+ "description": "PMC ID — present for NCBI PMC records and Europe PMC entries that have a PMC counterpart. Absent for EPMC-only records like preprints; use `epmcId` in that case.",
+ "type": "string"
+ },
+ "pmcUrl": {
+ "description": "PMC URL — derived from `pmcId` when present",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID",
+ "type": "string"
+ },
+ "publicationDate": {
+ "additionalProperties": false,
+ "description": "Publication date",
+ "properties": {
+ "day": {
+ "description": "Publication day",
+ "type": "string"
+ },
+ "month": {
+ "description": "Publication month",
+ "type": "string"
+ },
+ "year": {
+ "description": "Publication year",
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL",
+ "type": "string"
+ },
+ "references": {
+ "description": "Reference list",
+ "items": {
+ "additionalProperties": false,
+ "description": "Reference entry",
+ "properties": {
+ "citation": {
+ "description": "Citation text",
+ "type": "string"
+ },
+ "id": {
+ "description": "Reference ID",
+ "type": "string"
+ },
+ "label": {
+ "description": "Reference label",
+ "type": "string"
+ }
+ },
+ "required": [
+ "citation"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "sections": {
+ "description": "Article body sections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article body section",
+ "properties": {
+ "label": {
+ "description": "Section label",
+ "type": "string"
+ },
+ "subsections": {
+ "description": "Nested subsections",
+ "items": {
+ "additionalProperties": false,
+ "description": "Article subsection",
+ "properties": {
+ "label": {
+ "description": "Subsection label",
+ "type": "string"
+ },
+ "text": {
+ "description": "Subsection body text. Sections nested deeper than this level are folded in here in document order, each heading rendered on its own line above its text.",
+ "type": "string"
+ },
+ "title": {
+ "description": "Subsection heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "text": {
+ "description": "Section body text",
+ "type": "string"
+ },
+ "title": {
+ "description": "Section heading",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "source": {
+ "const": "pmc",
+ "description": "Structured JATS — same DTD whether sourced from NCBI PMC or Europe PMC",
+ "type": "string"
+ },
+ "title": {
+ "description": "Article title",
+ "type": "string"
+ },
+ "viaSource": {
+ "description": "Which layer produced the JATS: `pmc` for NCBI PMC EFetch (db=pmc), `europepmc` for Europe PMC `fullTextXML`. Both paths return the same JATS shape; the discriminator records origin for observability and license attribution.",
+ "enum": [
+ "pmc",
+ "europepmc"
+ ],
+ "type": "string"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "sections"
+ ],
+ "type": "object"
+ },
+ {
+ "additionalProperties": false,
+ "description": "Best-effort full text from an open-access copy",
+ "properties": {
+ "content": {
+ "description": "Full article text — Markdown or plain text per `contentFormat`",
+ "type": "string"
+ },
+ "contentFormat": {
+ "description": "How `content` was extracted. html-markdown: Defuddle extracted Markdown from an HTML landing page; light section structure may survive but is not guaranteed. pdf-text: unpdf extracted plain text from a PDF; no section, reference, or heading structure.",
+ "enum": [
+ "html-markdown",
+ "pdf-text"
+ ],
+ "type": "string"
+ },
+ "doi": {
+ "description": "DOI used to locate the open-access copy",
+ "type": "string"
+ },
+ "hostType": {
+ "description": "`publisher` or `repository` — where the OA copy is hosted",
+ "type": "string"
+ },
+ "license": {
+ "description": "License identifier from Unpaywall (e.g. cc-by, cc0)",
+ "type": "string"
+ },
+ "pmcId": {
+ "description": "PMC ID this article was requested under, in `PMC<digits>` form — present for `pmcids` input, absent for `pmids` and `dois` input. Ties the article back to the requested identifier, which `unavailable[]` keys on for the ids that found nothing.",
+ "type": "string"
+ },
+ "pmid": {
+ "description": "PubMed ID when input was `pmids`; absent for `pmcids` and `dois` input",
+ "type": "string"
+ },
+ "pubmedUrl": {
+ "description": "PubMed URL — present when `pmid` is set",
+ "type": "string"
+ },
+ "source": {
+ "const": "unpaywall",
+ "description": "Content fetched from an open-access copy indexed by Unpaywall. Best-effort — structural fidelity depends on `contentFormat`.",
+ "type": "string"
+ },
+ "sourceUrl": {
+ "description": "URL the content was fetched from",
+ "type": "string"
+ },
+ "title": {
+ "description": "Detected article title when present",
+ "type": "string"
+ },
+ "totalPages": {
+ "description": "Page count reported by the PDF extractor; absent for HTML",
+ "type": "number"
+ },
+ "version": {
+ "description": "OA version: submittedVersion | acceptedVersion | publishedVersion",
+ "type": "string"
+ },
+ "viaSource": {
+ "const": "unpaywall",
+ "description": "Layer that produced this article. Constant `unpaywall` for this branch.",
+ "type": "string"
+ },
+ "wordCount": {
+ "description": "Approximate word count reported by the HTML extractor; absent for PDFs",
+ "type": "number"
+ }
+ },
+ "required": [
+ "source",
+ "viaSource",
+ "contentFormat",
+ "doi",
+ "sourceUrl",
+ "content"
+ ],
+ "type": "object"
+ }
+]pubmed_fetch_articles6 fields changedInput schema / properties / maxResponseCharactersAdded value: +{
+ "description": "Opt-in ceiling for the whole response, in characters. Each article is measured as the JSON record it is returned as — title, abstract, authors, journal, MeSH terms, grants, identifiers, every field it carries. Articles are kept in response order until the next one would cross the ceiling; that article and the rest are deferred whole (never partially populated) and listed in `deferred.ids`. Response envelope fields — counts, `unavailablePmids`, `deferred` itself — are not counted. Omit to return every resolved article.",
+ "maximum": 1000000,
+ "minimum": 1,
+ "type": "integer"
+}Output schema / properties / deferredAdded value: +{
+ "additionalProperties": false,
+ "description": "Continuation state for articles the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one article.",
+ "properties": {
+ "deferredCount": {
+ "description": "Articles that resolved but were withheld to stay under the ceiling",
+ "type": "number"
+ },
+ "ids": {
+ "description": "PMIDs of the deferred articles, in response order. Re-call `pubmed_fetch_articles` with these as `pmids` and the same other inputs to retrieve them. Never contains a PMID from `unavailablePmids`.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "maxResponseCharacters": {
+ "description": "The `maxResponseCharacters` ceiling this response was budgeted against",
+ "type": "number"
+ },
+ "nextDeferredCharacters": {
+ "description": "Serialized size of the next deferred article — the first entry in `ids`, where the response stopped. Raise `maxResponseCharacters` to at least this to make progress; a smaller article further down `ids` cannot be reached until this one fits.",
+ "type": "number"
+ },
+ "returnedCharacters": {
+ "description": "Serialized characters the returned article records account for",
+ "type": "number"
+ }
+ },
+ "required": [
+ "maxResponseCharacters",
+ "returnedCharacters",
+ "deferredCount",
+ "ids",
+ "nextDeferredCharacters"
+ ],
+ "type": "object"
+}Output schema / properties / notice / descriptionPrevious value: -"Optional guidance when no articles were returned — points to discovery tools. Absent on successful fetches."New value: +"Optional guidance when no articles were returned — points to discovery tools — or when `maxResponseCharacters` deferred articles, naming how to retrieve them. Absent on successful unbudgeted fetches."Output schema / properties / totalReturned / descriptionPrevious value: -"Number of articles returned"New value: +"Number of articles in this response. Under a `maxResponseCharacters` budget this counts the kept articles only; `deferred.deferredCount` covers the rest."Output schema / properties / truncatedAdded value: +{
+ "description": "True when `maxResponseCharacters` withheld at least one resolved article. Absent when the response carries every article that resolved. The continuation state is in `deferred`.",
+ "type": "boolean"
+}Output schema / properties / unavailablePmids / descriptionPrevious value: -"PMIDs that returned no article data"New value: +"PMIDs that returned no article data. Reported in full regardless of where a `maxResponseCharacters` cutoff lands — these are misses, not deferrals, and re-requesting them returns nothing."pubmed_fetch_fulltext9 fields changedInput schema / properties / maxCharacters / descriptionPrevious value: -"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text, or the `source=unpaywall` `content` body; titles, abstracts, identifiers, and references are never counted or shortened. Applied after `sections`, `maxSections`, and `includeReferences`, so semantic filtering is unaffected. The response-wide ceiling is this value times the number of articles returned. Omit for the full body."New value: +"Per-article budget for body text, in characters. Counts `source=pmc` section and subsection text, or the `source=unpaywall` `content` body; titles, abstracts, identifiers, and references are never counted or shortened. Applied after `sections`, `maxSections`, and `includeReferences`, so semantic filtering is unaffected. This knob alone bounds only bodies: the response-wide ceiling it implies is this value times the number of articles returned, plus every uncounted field. Use `maxResponseCharacters` for a true whole-response ceiling. Omit for the full body."Input schema / properties / maxResponseCharactersAdded value: +{
+ "description": "Opt-in ceiling for the whole response, in characters — the true response-wide counterpart to the per-article `maxCharacters`. Each article is measured as the JSON record it is returned as, after every filter and the per-article body budget: title, abstract, body sections, references, identifiers, license and source metadata — every field it carries. One ledger covers all tiers, so PMC-, Europe PMC-, and Unpaywall-served articles spend the same budget. Articles are kept in response order until the next one would cross the ceiling; that article and the rest are deferred whole (never partially populated) and listed in `deferred.ids`. Response envelope fields — counts, `unavailable`, `truncation`, `deferred` itself — are not counted. Omit to return every resolved article.",
+ "maximum": 1000000,
+ "minimum": 1,
+ "type": "integer"
+}Output schema / properties / deferredAdded value: +{
+ "additionalProperties": false,
+ "description": "Continuation state for articles the whole-response budget withheld. Present only when `maxResponseCharacters` deferred at least one article.",
+ "properties": {
+ "deferredCount": {
+ "description": "Articles the chain resolved but withheld to stay under the ceiling",
+ "type": "number"
+ },
+ "idType": {
+ "description": "Which input branch the deferred ids belong to — re-submit them as `pmids`, `pmcids`, or `dois` respectively. Matches the `idType` on `unavailable` entries.",
+ "enum": [
+ "pmid",
+ "pmcid",
+ "doi"
+ ],
+ "type": "string"
+ },
+ "ids": {
+ "description": "Identifiers of the deferred articles, in response order, keyed as they were requested (PMC IDs in `PMC<digits>` form). Re-call `pubmed_fetch_fulltext` with these under the `idType` branch and the same other inputs. Never contains an id from `unavailable`.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "maxResponseCharacters": {
+ "description": "The `maxResponseCharacters` ceiling this response was budgeted against",
+ "type": "number"
+ },
+ "nextDeferredCharacters": {
+ "description": "Serialized size of the next deferred article — the first entry in `ids`, where the response stopped. Raise `maxResponseCharacters` to at least this to make progress; a smaller article further down `ids` cannot be reached until this one fits.",
+ "type": "number"
+ },
+ "returnedCharacters": {
+ "description": "Serialized characters the returned article records account for",
+ "type": "number"
+ }
+ },
+ "required": [
+ "maxResponseCharacters",
+ "returnedCharacters",
+ "deferredCount",
+ "idType",
+ "ids",
+ "nextDeferredCharacters"
+ ],
+ "type": "object"
+}Output schema / properties / notice / descriptionPrevious value: -"Optional guidance for a partial or empty body. A `sections`-filter miss names the requested terms and affected article id(s) and suggests retrying without `sections` or using broader headings. A metadata-only record names the id(s) the chain could retrieve as front matter only and points at `pubmed_fetch_articles` for the abstract. A budgeted response names the characters returned versus carried and points at `truncation`. Absent when none of those applies."New value: +"Optional guidance for a partial or empty body. A `sections`-filter miss names the requested terms and affected article id(s) and suggests retrying without `sections` or using broader headings. A metadata-only record names the id(s) the chain could retrieve as front matter only and points at `pubmed_fetch_articles` for the abstract. A budgeted response names the characters returned versus carried and points at `truncation`. A response-wide budget that deferred articles names the ids to re-request. Absent when none of those applies."Output schema / properties / totalReturned / descriptionPrevious value: -"Number of articles returned"New value: +"Number of articles in this response. Under a `maxResponseCharacters` budget this counts the kept articles only; `deferred.deferredCount` covers the rest."Output schema / properties / truncated / descriptionPrevious value: -"True when a character budget shortened at least one returned body. Absent when every returned article carries its full post-filter body. The per-article accounting is in `truncation`."New value: +"True when a character budget shortened at least one returned body, or withheld a whole article. Absent when every resolved article is present with its full post-filter body. The per-article body accounting is in `truncation`; the withheld ids are in `deferred`."Output schema / properties / unavailable / descriptionPrevious value: -"Per-identifier explanations for any requested PMIDs, PMCIDs, or DOIs with no returnable full text. `idType` discriminates which branch the id came from."New value: +"Per-identifier explanations for any requested PMIDs, PMCIDs, or DOIs with no returnable full text. `idType` discriminates which branch the id came from. Distinct from `deferred`: nothing here is retrievable by re-calling, and an id never appears in both."Output schema / properties / unavailable / items / properties / reason / descriptionPrevious value: -"Why no full text was returned. not-found: upstream returned no record for this ID. no-pmc-fallback-disabled: every tier was skipped (`triedTiers` is all `not-attempted`) — typically because EPMC (`EUROPEPMC_ENABLED`) and Unpaywall (`UNPAYWALL_EMAIL`) are not configured. no-epmc-fulltext: EPMC indexed the record but publishes no fullTextXML. no-body: the record was retrieved but carries front matter and abstract only, with no body sections — use `pubmed_fetch_articles` for the metadata. no-doi: no DOI to query Unpaywall. no-oa: Unpaywall has no OA copy. fetch-failed: download failed. parse-failed: extraction empty. service-error: upstream server failure (threw, timed out, or returned malformed data)."New value: +"Why no full text was returned — the most specific signal any tier that answered reported. not-found: upstream returned no record for this ID. no-pmc-fallback-disabled: every tier was skipped (`triedTiers` is all `not-attempted`) — typically because EPMC (`EUROPEPMC_ENABLED`) and Unpaywall (`UNPAYWALL_EMAIL`) are not configured. no-epmc-fulltext: EPMC indexed the record but publishes no fullTextXML. no-body: the record was retrieved but carries front matter and abstract only, with no body sections — use `pubmed_fetch_articles` for the metadata. no-doi: no DOI to query Unpaywall. no-oa: Unpaywall has no OA copy. fetch-failed: download failed. parse-failed: extraction empty. service-error: upstream server failure (threw, timed out, or returned malformed data). A reason never means the chain ran to completion — read `unqueriedTiers` for that."Output schema / properties / unavailable / items / properties / unqueriedTiersAdded value: +{
+ "description": "Tiers the chain skipped because this deployment has not configured them, and that could have served this id — the search was incomplete, and a deployment with these tiers configured may still resolve the id. `triedTiers` carries which environment variable each one is waiting on. Absent when every tier that could have served the id was actually queried; a tier skipped because it was inapplicable to this id (no DOI for Unpaywall) is never listed.",
+ "items": {
+ "description": "A fallback tier this deployment has not configured",
+ "enum": [
+ "europepmc",
+ "unpaywall"
+ ],
+ "type": "string"
+ },
+ "type": "array"
+}pubmed_europepmc_fetch3 fields changedOutput schema / properties / records / items / properties / authors / descriptionPrevious value: -"Formatted author string"New value: +"Formatted author string as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."Output schema / properties / records / items / properties / journal / descriptionPrevious value: -"Journal title"New value: +"Journal title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."Output schema / properties / records / items / properties / title / descriptionPrevious value: -"Record title"New value: +"Record title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."pubmed_europepmc_search3 fields changedOutput schema / properties / hits / items / properties / authors / descriptionPrevious value: -"Formatted author string"New value: +"Formatted author string as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."Output schema / properties / hits / items / properties / journal / descriptionPrevious value: -"Journal title"New value: +"Journal title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."Output schema / properties / hits / items / properties / title / descriptionPrevious value: -"Article title"New value: +"Article title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded."pubmed_find_related4 fields changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `openalex_unreachable`: OpenAlex was unreachable after all retry attempts. `openalex_invalid_response`: OpenAlex returned a body that could not be parsed (invalid JSON). Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `openalex_unreachable`: OpenAlex was unreachable after all retry attempts. `openalex_invalid_response`: OpenAlex returned a body that could not be parsed (invalid JSON). `all_providers_failed`: Every provider eligible for the requested relationship failed; none answered. Other values are possible when a failure originates below the handler."Output schema / properties / error / properties / data / properties / reason / examplesPrevious value: -[
- "queue_full",
- "ncbi_unreachable",
- "ncbi_deadline_exceeded",
- "ncbi_invalid_response",
- "ncbi_resource_not_found",
- "europepmc_unreachable",
- "europepmc_invalid_response",
- "europepmc_invalid_input",
- "openalex_unreachable",
- "openalex_invalid_response"
-]New value: +[
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "europepmc_unreachable",
+ "europepmc_invalid_response",
+ "europepmc_invalid_input",
+ "openalex_unreachable",
+ "openalex_invalid_response",
+ "all_providers_failed"
+]Output schema / properties / notice / descriptionPrevious value: -"Guidance when results are empty, a fallback provider answered, or offset overshot. Absent on a clean NCBI result page."New value: +"Guidance when results are empty, a fallback provider answered, offset overshot, or Europe PMC rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page."Output schema / properties / totalCount / descriptionPrevious value: -"Total related articles found before windowing"New value: +"Total related articles found before windowing. A Europe PMC total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned."pubmed_convert_ids6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "records",
+ "totalConverted",
+ "totalSubmitted"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "records",
- "totalConverted",
- "totalSubmitted"
-]pubmed_europepmc_fetch6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "records"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "europepmc_unreachable",
+ "europepmc_invalid_response",
+ "europepmc_invalid_input",
+ "europepmc_disabled"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "records"
-]pubmed_europepmc_search6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "hits",
+ "cursorMark",
+ "searchUrl",
+ "query",
+ "totalCount",
+ "appliedSources"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "europepmc_unreachable",
+ "europepmc_invalid_response",
+ "europepmc_invalid_input",
+ "europepmc_disabled"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "hits",
- "cursorMark",
- "searchUrl",
- "query",
- "totalCount",
- "appliedSources"
-]pubmed_fetch_articles6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "articles",
+ "totalReturned"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `invalid_efetch_response`: NCBI EFetch returned a payload missing the PubmedArticleSet wrapper. Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "invalid_efetch_response"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "articles",
- "totalReturned"
-]pubmed_fetch_fulltext7 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "articles",
+ "totalReturned"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `unpaywall_unreachable`: Unpaywall was unreachable when resolving a DOI or fetching content. `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "unpaywall_unreachable",
+ "europepmc_unreachable",
+ "europepmc_invalid_response",
+ "europepmc_invalid_input"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / properties / truncatedAdded value: +{
+ "description": "True when a character budget shortened at least one returned body. Absent when every returned article carries its full post-filter body. The per-article accounting is in `truncation`.",
+ "type": "boolean"
+}Output schema / requiredRemoved value: -[
- "articles",
- "totalReturned"
-]pubmed_find_related6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "sourcePmid",
+ "relationship",
+ "offset",
+ "articles",
+ "totalCount",
+ "source"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). `europepmc_unreachable`: Europe PMC was unreachable after all retry attempts. `europepmc_invalid_response`: Europe PMC returned a body that could not be parsed (invalid JSON or XML). `europepmc_invalid_input`: Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter). `openalex_unreachable`: OpenAlex was unreachable after all retry attempts. `openalex_invalid_response`: OpenAlex returned a body that could not be parsed (invalid JSON). Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found",
+ "europepmc_unreachable",
+ "europepmc_invalid_response",
+ "europepmc_invalid_input",
+ "openalex_unreachable",
+ "openalex_invalid_response"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "sourcePmid",
- "relationship",
- "offset",
- "articles",
- "totalCount",
- "source"
-]pubmed_format_citations6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "citations",
+ "totalSubmitted",
+ "totalFormatted"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "citations",
- "totalSubmitted",
- "totalFormatted"
-]pubmed_lookup_citation6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "results",
+ "totalMatched",
+ "totalSubmitted",
+ "totalWarnings"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "results",
- "totalMatched",
- "totalSubmitted",
- "totalWarnings"
-]pubmed_lookup_mesh6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "query",
+ "offset",
+ "results",
+ "totalCount"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "query",
- "offset",
- "results",
- "totalCount"
-]pubmed_search_articles6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "query",
+ "offset",
+ "pmids",
+ "summaries",
+ "searchUrl",
+ "effectiveQuery",
+ "totalCount",
+ "appliedFilters"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "query",
- "offset",
- "pmids",
- "summaries",
- "searchUrl",
- "effectiveQuery",
- "totalCount",
- "appliedFilters"
-]pubmed_spell_check6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "original",
+ "corrected",
+ "hasSuggestion"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded value: +{
+ "additionalProperties": {},
+ "description": "Present when the call failed. Absent on success.",
+ "properties": {
+ "code": {
+ "description": "JSON-RPC error code for this failure.",
+ "maximum": 9007199254740991,
+ "minimum": -9007199254740991,
+ "type": "integer"
+ },
+ "data": {
+ "additionalProperties": {},
+ "properties": {
+ "reason": {
+ "description": "Machine-readable failure mode. Declared by this tool: `queue_full`: Local NCBI request queue is at capacity. `ncbi_unreachable`: NCBI E-utilities is unreachable after all retry attempts. `ncbi_deadline_exceeded`: Total request deadline expired before NCBI returned a response. `ncbi_invalid_response`: NCBI returned a body that could not be parsed (invalid XML/JSON). `ncbi_resource_not_found`: NCBI returned a structured \"not found\" error for the requested ID(s). Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "queue_full",
+ "ncbi_unreachable",
+ "ncbi_deadline_exceeded",
+ "ncbi_invalid_response",
+ "ncbi_resource_not_found"
+ ],
+ "type": "string"
+ },
+ "recovery": {
+ "additionalProperties": {},
+ "description": "Actionable next step for the caller.",
+ "properties": {
+ "hint": {
+ "type": "string"
+ }
+ },
+ "required": [
+ "hint"
+ ],
+ "type": "object"
+ },
+ "retryable": {
+ "description": "Whether retrying may succeed.",
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "message": {
+ "description": "Human-readable description of what went wrong.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "message"
+ ],
+ "type": "object"
+}Output schema / requiredRemoved value: -[
- "original",
- "corrected",
- "hasSuggestion"
-]Search biomedical literature, get article details, find related articles, and explore MeSH terms
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PubMed MCP — wraps the NCBI E-utilities API (biomedical literature, free, no auth)
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