pubmed-mcp-server
pubmed-mcp-server is an MCP server for searching, retrieving, and citing biomedical literature from PubMed, PubMed Central, Europe PMC, OpenAlex, and Unpaywall.
Search PubMed (
pubmed_search_articles) with full NCBI query syntax plus structured filters (author, journal, MeSH, publication type, language, species, abstract, free full text), date ranges, sorting, and offset pagination — returns PMIDs, total counts, the effective query, and applied filters.Fetch article metadata (
pubmed_fetch_articles) by up to 200 PMIDs: abstracts, authors, journal info, DOI/PMC IDs, MeSH terms, grants, publication types, retraction/correction notices, Bookshelf book and chapter records, and optional response-size budgeting that defers overflow articles.Get full text (
pubmed_fetch_fulltext) by PMID, PMCID, or DOI, falling back PMC → Europe PMC → Unpaywall, with structured sections, tables, figures, references, section filtering, and character budgets.Search Europe PMC (
pubmed_europepmc_search) for preprints, patents, and Agricola records PubMed doesn't carry, with cursor pagination.Fetch complete Europe PMC records (
pubmed_europepmc_fetch) bysource+epmcIdto get untruncated abstracts.Format citations (
pubmed_format_citations) in APA, MLA, BibTeX, RIS, and Vancouver.Find related articles (
pubmed_find_related): similar content, citing articles, or references, with NCBI → Europe PMC → OpenAlex fallback.Correct queries (
pubmed_spell_check) via NCBI ESpell after zero-hit or thin searches.Explore MeSH vocabulary (
pubmed_lookup_mesh) for descriptors, tree numbers, scope notes, and entry terms.Resolve partial citations to PMIDs (
pubmed_lookup_citation, up to 25 at a time via ECitMatch).Convert identifiers (
pubmed_convert_ids) between DOI, PMID, and PMCID for PMC-indexed articles.Inspect database metadata via the
pubmed://database/inforesource (field list, record count, last update).Generate a structured four-phase research plan with the
research_planprompt.Connect flexibly: stdio, local Streamable HTTP, or the public hosted endpoint, with optional NCBI/Unpaywall API keys and configurable providers.
Connects AI agents to NCBI's PubMed and E-utilities, enabling search, retrieval, and analysis of biomedical literature. Provides tools for searching articles, fetching detailed content, finding related articles, generating citations, creating research plans, and visualizing data through charts.
Generates SVG chart visualizations from PubMed data, supporting bar, line, and scatter chart types for data representation.
Built with TypeScript for type safety and robust input validation, ensuring secure and reliable interactions with PubMed's biomedical data.
Utilizes Vega-Lite specifications to render SVG charts from PubMed data, enabling visualization of biomedical research trends and statistics.
Processes PubMed article data in XML format, providing JSON representation of the PubMedArticle XML structure through the fetch_pubmed_content tool.
Uses Zod for schema validation of inputs and outputs when interacting with PubMed, ensuring type safety and proper data formatting.
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@pubmed-mcp-serversearch for recent articles about CRISPR gene editing in cancer therapy"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
Public Hosted Server: https://pubmed.caseyjhand.com/mcp
Overview
Biomedical literature from PubMed, PubMed Central, and Europe PMC. Search it, fetch metadata and full text, resolve identifiers and partial citations, format references, and ground queries in MeSH vocabulary. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.
Tools
Tool | Description |
| Search PubMed with full query syntax, structured filters, date ranges, and optional summaries |
| Fetch article metadata by PMID: abstract, authors, journal, MeSH terms, grants, linked retraction and correction notices |
| Fetch full text by PMID, PMCID, or DOI, falling back from PMC to Europe PMC to Unpaywall |
| Search Europe PMC for preprints, patents, Agricola, and open-access records PubMed doesn't carry |
| Fetch complete Europe PMC records, including the untruncated abstract, by |
| Format citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM) |
| Find similar articles, citing articles, or references for a PMID |
| Correct a misspelled PubMed query via NCBI ESpell |
| Look up MeSH headings with tree numbers, scope notes, and entry terms |
| Resolve partial references, up to 25 at a time, to PMIDs via ECitMatch |
| Convert between DOI, PMID, and PMCID via the PMC ID Converter |
Resources
Resource | Description |
| PubMed database metadata via EInfo (field list, record count, last update) |
Prompts
Prompt | Description |
| Generate a structured four-phase biomedical research plan |
Related MCP server: PubMed MCP Server
Capability reference
pubmed_search_articles tool
Full PubMed query syntax plus filters (author, journal, MeSH, publication type, language, species, abstract, free full text) and publication/modification/Entrez date ranges
Up to 1,000 results per page and offsets up to 9,998;
summaryCountadds briefs for up to 50 hitsReports
totalCount, theeffectiveQueryPubMed ran, and theappliedFiltersRejects blank filter values, impossible dates, and reversed date ranges before PubMed is called
pubmed_fetch_articles tool
Up to 200 PMIDs per call; misses are listed in
unavailablePmidsAbstract, authors, journal, DOI, publication types, linked retraction/erratum/comment notices, and links; MeSH terms on by default, grants via
includeGrantsrecordTypeseparates journal articles from Bookshelf chapters and books; opt-inmaxResponseCharactersdefers overflow todeferred.ids
pubmed_fetch_fulltext tool
One of
pmcids,pmids, ordois, up to 10 per call, tried against PMC, then Europe PMC, then Unpaywall (needsUNPAYWALL_EMAIL);viaSourcenames the tier that answeredsource: "pmc"returns sections, tables, and figures;source: "unpaywall"returns a best-effort HTML or PDF text bodyMisses carry a typed
reasonandtriedTiers;sections,maxCharacters,overflowMode, andmaxResponseCharactersbound the response, andtruncationreports what was cut
pubmed_europepmc_search tool
Adds preprints (
PPR), patents (PAT), and Agricola (AGR) toMEDandPMC; defaults toMED,PMC,PPRCursor pagination via
cursorMark/nextCursorMark, up to 100 per page; abstracts arrive as 400-character snippetsNot registered when
EUROPEPMC_ENABLED=false
pubmed_europepmc_fetch tool
Up to 25 records per call, addressed by a search hit's
source+epmcId, with the full abstract; unresolved ids land innotFoundNot registered when
EUROPEPMC_ENABLED=false
pubmed_format_citations tool
Up to 50 PMIDs per call, in any mix of
apa,mla,bibtex,ris, andvancouverBookshelf records cite as edited books; PMIDs that can't be fetched are reported as unavailable
pubmed_find_related tool
similar,cited_by, orreferences, up to 50 per page with offset paginationFalls back to Europe PMC, then OpenAlex, and names the provider that answered; fails as
all_providers_failedif none can
pubmed_spell_check tool
Returns
original,corrected, andhasSuggestion, fixing every misspelled token in one callRun it after a zero-hit or thin search, then retry
pubmed_search_articleswithcorrected
pubmed_lookup_mesh tool
Descriptors by name or free-text term, with an exact heading match pinned first; up to 50 per page, continued via
nextOffsetRecords carry
meshId;includeDetails(default on) adds tree numbers, scope notes, and entry terms
pubmed_lookup_citation tool
Up to 25 partial citations per call; journal or year is required, and volume, first page, and author sharpen the match
Each comes back
matched,not_found, orambiguous, with recovery detail
pubmed_convert_ids tool
Up to 50 ids per call, all of one declared
idType(doi,pmid,pmcid); only PMC-indexed articles resolveOne success or error row per id, in order, so a partial batch never fails
pubmed://database/info resource
Live EInfo call for the
pubmeddatabase, returned asapplication/jsoncount,lastUpdate, andfields[], whose names are the search tagspubmed_search_articlesaccepts
research_plan prompt
Arguments:
title,goal, andkeywordsrequired;organismandincludeAgentPromptsoptionalReturns a four-phase research plan;
includeAgentPrompts: "true"adds an agent-guidance block under each of its nine sub-steps, two of which point at tools: the literature review namespubmed_search_articlesandpubmed_lookup_mesh, and the interpretation step namespubmed_search_articles
Features
Built on @cyanheads/mcp-ts-core: stdio and Streamable HTTP transports, pluggable auth (none / jwt / oauth), swappable storage (in-memory, filesystem, Supabase, Cloudflare KV/R2/D1), structured logging with optional OpenTelemetry tracing.
PubMed-specific:
NCBI E-utilities (ESearch, EFetch, ESummary, ELink, ESpell, EInfo, ECitMatch) and the PMC ID Converter, with Europe PMC, OpenAlex, and Unpaywall filling the gaps
Shared NCBI request queue: paced request starts, capped concurrency, a cooldown that holds every caller after an NCBI 429, and one deadline covering queue wait and retries
XML parsing built for PubMed's inconsistent records: structured abstracts, missing fields, varying date formats
Forgiving identifiers: a zero-padded PMID resolves as the PMID it spells in every tool that takes one;
pubmed_fetch_fulltextalso matches DOIs case-insensitively and PMC IDs with or without thePMCprefixHand-rolled citation formatters (APA, MLA, BibTeX, RIS, Vancouver) with no dependencies
Agent-friendly output:
Provenance on every response: source labels, license fields, best-effort warnings on Unpaywall results, and effective-query echo on searches, so agents can judge what to trust
Graceful partial failure: batch tools return per-item success/error rows instead of failing the request, with structured status codes and actionable next-step text
Discriminated output contracts:
source: "pmc" | "unpaywall", typedunavailablereasons,viaSourceandtriedTiersfields, so callers branch on data, not string parsing
Getting started
Public Hosted Instance
A public instance is available at https://pubmed.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:
{
"mcpServers": {
"pubmed-mcp-server": {
"type": "streamable-http",
"url": "https://pubmed.caseyjhand.com/mcp"
}
}
}Self-Hosted / Local
Add the following to your MCP client configuration file.
{
"mcpServers": {
"pubmed-mcp-server": {
"type": "stdio",
"command": "bunx",
"args": ["@cyanheads/pubmed-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio",
"MCP_LOG_LEVEL": "info",
"NCBI_API_KEY": "your-key-here"
}
}
}
}Or with npx (no Bun required):
{
"mcpServers": {
"pubmed-mcp-server": {
"type": "stdio",
"command": "npx",
"args": ["-y", "@cyanheads/pubmed-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio",
"MCP_LOG_LEVEL": "info",
"NCBI_API_KEY": "your-key-here"
}
}
}
}Or with Docker:
{
"mcpServers": {
"pubmed-mcp-server": {
"type": "stdio",
"command": "docker",
"args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/pubmed-mcp-server:latest"]
}
}
}For Streamable HTTP, set the transport and start the server:
MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcpPrerequisites
Bun v1.4.0 or higher (or Node.js v24+).
Optional: an NCBI API key raises the rate limit from 3 to 10 requests per second.
Installation
Clone the repository:
git clone https://github.com/cyanheads/pubmed-mcp-server.gitNavigate into the directory:
cd pubmed-mcp-serverInstall dependencies:
bun installConfigure environment:
cp .env.example .env
# edit .env and set NCBI_API_KEY, NCBI_ADMIN_EMAIL, and UNPAYWALL_EMAIL as neededConfiguration
Variable | Description | Default |
| NCBI API key; raises the rate limit from 3 to 10 req/s. | none |
| Contact email sent with NCBI requests, as NCBI recommends. | none |
| Minimum gap between NCBI request starts, in ms. |
|
| Max concurrent in-flight NCBI requests. |
|
| Retry attempts for failed NCBI requests. |
|
| Per-request HTTP timeout, in ms. |
|
| Deadline for one NCBI call across queue wait, retries, and backoff, in ms. A call that can't start in time is rejected at once. |
|
| Contact email for Unpaywall. Setting it enables the Unpaywall tier of | none |
| Per-request timeout for Unpaywall lookups and content fetches, in ms. |
|
| Set |
|
| Optional contact email sent with Europe PMC requests. | none |
| Minimum gap between Europe PMC request starts, in ms. |
|
| Retry attempts for failed Europe PMC requests. |
|
| Per-request timeout for Europe PMC calls, in ms. |
|
| Transport: |
|
| HTTP server port. |
|
| HTTP session mode: |
|
| Authentication: |
|
| Log level ( |
|
| Directory for log files (Node.js only). |
|
| Storage backend: |
|
| Enable OpenTelemetry. |
|
See .env.example for every server setting and the common framework overrides.
Running the server
Local development
Build and run the production version:
# One-time build bun run rebuild # Run the built server bun run start:http # or bun run start:stdioRun checks and tests:
bun run devcheck # Lints, formats, type-checks, and more bun run test # Runs the test suite
Project structure
Directory | Purpose |
| Tool definitions ( |
| Resource definitions. Database info resource. |
| Prompt definitions. Research plan prompt. |
| NCBI E-utilities service layer — API client, queue, parser, formatter. |
| Europe PMC service — search + |
| Unpaywall service — DOI → OA location resolution and content fetch (HTML/PDF). |
| OpenAlex service — last-resort provider for |
| Server-specific environment variable parsing and validation with Zod. |
| Unit and integration tests, mirroring the |
Development guide
See CLAUDE.md for development guidelines and architectural rules. The short version:
Handlers throw, framework catches — no
try/catchin tool logicUse
ctx.logfor logging,ctx.statefor storageRegister new tools and resources in the
createApp()arrays insrc/index.tsWrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields
Contributing
Issues are welcome. Run checks and tests before submitting:
bun run devcheck
bun run testLicense
This project is licensed under the Apache 2.0 License. See the LICENSE file for details.
Available Tools
11 toolspubmed_convert_idsPubmed Convert IdsARead-onlyInspect
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. |
Output Schema
| 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 |
TDQS
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.
pubmed_europepmc_fetchPubmed Europepmc FetchARead-onlyInspect
Fetch complete Europe PMC records — including the full, untruncated abstract — for records addressed by source plus epmcId. Pairs with pubmed_europepmc_search, which returns bounded abstractSnippet values and flags cut ones with abstractTruncated: true; pass those hits' source and epmcId 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.
| 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. |
Output Schema
| 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. Absent when every record came back. |
| records | No | Resolved records, in the order Europe PMC returned them |
| notFound | No | Requested `source` + `epmcId` pairs Europe PMC returned no record for |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint and openWorldHint, so the safety profile is covered. The description adds real behavioral context beyond them: up to 25 records per call, the whole batch resolving in a single Europe PMC request, and that abstracts come back untruncated. Auth requirements and any rate-limit behavior are not stated, keeping it short of a 5.
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, then the truncation/pairing rationale, then the record-count limit. Every sentence carries distinct information; no 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, the description need not explain return values, and it still flags the key payload property (full abstract). For a one-parameter, read-only batch fetch it covers purpose, routing, and limits adequately.
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?
The single nested parameter is documented at 100% schema coverage, so the schema carries most of the load. The description still adds value by framing the pair as an address and pointing at where the values come from (the search hit's source and epmcId), plus the batch cap.
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') and immediately scopes it with the addressing model (source plus epmcId) and the full untruncated abstract. It explicitly distinguishes itself from pubmed_europepmc_search, pubmed_fetch_articles, and pubmed_fetch_fulltext by naming what each cannot do.
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?
Explicit routing: use this when search returns abstractTruncated: true, and this is the only retrieval path for PPR/PAT/AGR records that lack PMID and DOI. Names the alternative tools and the exact condition that rules them out, so nothing is left to inference.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
pubmed_europepmc_searchPubmed Europepmc SearchARead-onlyInspect
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’s source and epmcId to pubmed_europepmc_fetch 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). 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. | |
| 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 |
Output Schema
| 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. |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations cover only readOnly/openWorld; the description adds substantive behavior beyond them: default source set (MED, PMC, PPR), how to broaden with PAT/AGR, cursor-based pagination via cursorMark, and the fact that abstracts are returned bounded with abstractTruncated marking the cut ones. It also points to the fetch tool for full abstracts — genuinely useful disclosure not derivable from 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?
Dense but front-loaded: corpus scope, then sources, then pagination, then abstract handling. Every sentence carries information, though the sources default (MED/PMC/PPR) is stated twice — once in prose and once again in the same list — a minor redundancy.
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-value explanation is not owed, yet the description appropriately explains the one non-obvious output trait (bounded abstractSnippet / abstractTruncated) and supplies the recovery path to pubmed_europepmc_fetch. Combined with rich schema descriptions, an agent has everything needed to call this correctly.
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%, so the baseline is 3; the description still adds value by restating the sources default and the pattern for broadening coverage, plus the cursorMark pagination workflow (use '*' first, pass nextCursorMark verbatim). It does not explain sort or resultType semantics beyond the schema, so it is above baseline but not exhaustive.
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 Europe PMC, a broad open-access biomedical corpus') and immediately scopes it against siblings by enumerating the sources it spans (PPR, PAT, AGR, MED, PMC). An agent can distinguish it from pubmed_search_articles (PubMed-only) without opening either 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 a clear usage condition — 'Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery' — which implicitly routes agents here after pubmed_search_articles. It does not name the alternative sibling explicitly by tool name, so it stops short of a full when/when-not statement.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
pubmed_fetch_articlesPubmed Fetch ArticlesARead-onlyInspect
Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms, and linked retraction, erratum, and comment notices. 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 | |
| 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. |
Output Schema
| 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. |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint and openWorldHint, so the safety profile is covered; the description still adds real context by disclosing what the response contains and the truncation contract — articles past the ceiling are deferred whole, never partially populated, and surfaced in deferred.ids. That deferral semantics is behaviorally meaningful beyond the annotations.
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 tight sentences: purpose first, payload contents second, the truncation contract last. Every sentence carries information and none is redundant 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?
For a 4-parameter read tool with a full input schema and an output schema, the description supplies exactly the missing operational piece (how bulk responses are bounded and how to resume), and need not restate return fields because the output schema exists. Nothing required to invoke it correctly is absent.
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 each parameter already carries a thorough description, so the baseline is 3. The description restates the maxResponseCharacters/deferred.ids contract the schema already defines, adding no syntax or format detail the agent could not read from the schema.
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?
Specific verb + resource: 'Fetch full article metadata by PubMed IDs', with an enumeration of what the payload contains (abstract, authors, journal, MeSH terms, retraction/erratum/comment notices). The contrast with the sibling pubmed_fetch_fulltext is only implicit in the word 'metadata', so there is no explicit sibling differentiation.
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 implies when to use it (you have PMIDs and want their metadata) and explains the follow-up pattern for deferred IDs, but it never names an alternative or states exclusions. Nothing tells the agent when to pick this over pubmed_europepmc_fetch or pubmed_fetch_fulltext.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
pubmed_fetch_fulltextPubmed Fetch FulltextARead-onlyInspect
Fetch full-text articles from PubMed Central with structured sections, tables, and references. When PMC misses, transparently falls back to Europe PMC fullTextXML (structured JATS for records with a PMC counterpart). Provide exactly one of pmcids (PMC IDs directly), pmids (PubMed IDs, auto-resolved), or dois (DOIs, auto-resolved to PMC via the ID Converter; preprints with a PMC counterpart recover via Europe PMC). 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. 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. | |
| pmids | No | 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. | |
| pmcids | No | 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. | |
| 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". 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. | |
| maxSections | No | Maximum top-level body sections. 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. 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. 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. | |
| 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, 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. | |
| maxCharactersPerSection | No | 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. |
Output Schema
| 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. Absent when none of those applies. |
| articles | No | Full-text 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 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`. |
| 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` discriminates which branch the id came from. Distinct from `deferred`: nothing here is retrievable by re-calling, and an id never appears in both. |
| totalReturned | No | Number of articles in this response. Under a `maxResponseCharacters` budget this counts the kept articles only; `deferred.deferredCount` covers the rest. |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Goes well beyond the readOnly/openWorld annotations: it discloses the fallback tiers, what gets dropped (tables cut whole, sections omitted per overflowMode), that deferred articles are listed whole in deferred.ids, and that upstream layers may need UNPAYWALL_EMAIL. This is unusually rich behavioral disclosure for a read tool.
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?
Dense but front-loaded: purpose first, then fallback, then the exactly-one-of rule, then the budget knobs. Every sentence carries information relevant to calling the tool, though the packed clauses make it heavier than it needs to be for a summary.
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 12 parameters, an output schema, and safety annotations already present, the description supplies the missing conceptual glue: fallback behavior, the two independent character controls, and deferral semantics. Nothing an agent needs to invoke it correctly is absent.
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 every behavior the description summarizes (exactly-one-of the ID arrays, the two character budgets, overflow/deferral) is already spelled out in the per-parameter schema text. The description synthesizes the maxCharacters vs maxResponseCharacters distinction but adds little beyond the schema.
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 opening sentence gives a specific verb+resource+scope: "Fetch full-text articles from PubMed Central with structured sections, tables, and references," plus the fallback to Europe PMC. This clearly separates it from abstract-oriented siblings like pubmed_fetch_articles. It stops short of naming siblings (e.g. pubmed_europepmc_fetch) to disambiguate the full-text tools directly.
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?
Offers concrete invocation context: "Provide exactly one of pmcids, pmids, or dois" and explains the automatic fallback chain when PMC lacks full text. It does not, however, state when to prefer this over pubmed_europepmc_fetch or pubmed_fetch_articles, leaving sibling selection to inference.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
pubmed_format_citationsPubmed Format CitationsBRead-onlyInspect
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.
| 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 |
Output Schema
| 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. |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint and openWorldHint, so the safety profile is covered. The description adds no behavioral context of its own, such as whether unknown PMIDs are skipped, batching limits (max 50), or error handling, so beyond the safety hints it contributes little.
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 short sentences, front-loaded with the core action and ending with the parameter usage hint. Efficient, though the second sentence largely duplicates the schema's format description.
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 and parameters are fully documented, so the description need not explain return values. It is sufficient for correct invocation, with only routing guidance against siblings 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 coverage is 100% and both parameters carry their own descriptions, including the enum values and the string-vs-array duality. The description merely restates the format semantics already present in the schema, so the 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?
States a specific verb and resource ('Get formatted citations for PubMed articles') and enumerates supported styles, which is clear. It does not differentiate itself from the closest sibling pubmed_lookup_citation, so an agent must infer the boundary.
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?
No when-to-use guidance, no conditions, and no named alternatives. The reader gets no help deciding between this and pubmed_lookup_citation or pubmed_fetch_articles.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
pubmed_lookup_citationPubmed Lookup CitationARead-onlyInspect
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 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. |
Output Schema
| 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 |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations cover the safety profile (readOnlyHint, openWorldHint), and the description adds real behavioral depth: ECitMatch's journal+volume+page keying, the guarantee that author-only/volume-only inputs return no match, and that more fields improve accuracy. Return values are covered by the output schema, so nothing essential is missing.
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 dense sentences, front-loaded with purpose and followed by the differentiating rationale and input constraints. There is minor overlap between the description and the nested schema description ('more fields = better match accuracy'), but no wasted prose.
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 single-parameter batch lookup with 100% schema coverage and an output schema, the description supplies everything needed: purpose, alternatives comparison, hard input requirements, and batch semantics. Nothing an agent needs to invoke it correctly is absent.
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 each subfield is documented, so the baseline is 3; the description goes further by explaining the matching semantics — which field combinations are required versus which guarantee failure — adding meaning not visible from the schema alone.
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 (look up) and resource (PubMed IDs / PMIDs) from structured bibliographic citations, and explicitly differentiates itself from free-text alternatives ('more reliable than free-text search for structured references'), which maps to siblings like pubmed_search_articles.
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 triggering condition ('when you have a reference (journal, year, volume, page, author) and need the PMID') and states the input prerequisite (at least journal or year). It contrasts with free-text search but does not name sibling tools such as pubmed_search_articles or pubmed_convert_ids directly.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
pubmed_lookup_meshPubmed Lookup MeshARead-onlyInspect
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) |
Output Schema
| 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 |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations declare readOnlyHint and openWorldHint, so the safety profile is covered. The description adds useful behavioral context beyond that: what the records contain and the offset-based pagination 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, front-loaded with the core purpose, then the return shape and pagination. No wasted words.
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 needn't be spelled out; the description still summarizes the record contents and pagination cap. For a read-only lookup tool this is nearly complete, with usage routing the only notable gap.
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 thoroughly (including the nextOffset paging hint and the exact-match pinning to the first page). The description restates the pagination concept but adds no syntax or format detail beyond the schema, so the 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?
States a specific verb+resource: searching the MeSH controlled vocabulary, and names the returned record type (descriptor records with tree numbers, scope notes, entry terms). This is clearly distinguishable from the article-fetching and citation siblings, though it doesn't explicitly name them.
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 (look up MeSH terms) but the description never says when to prefer this over a free-text article search or any alternative. No explicit when/when-not or routing to sibling tools.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
pubmed_search_articlesPubmed Search ArticlesBRead-onlyInspect
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 | |
| 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. |
Output Schema
| 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 |
TDQS
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 with optional brief summaries) and the existence of offset paging, but omits the hard 9999-record ceiling and the rejection rules for malformed queries, both of which live only in 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, front-loaded with the verb and resource, then scope, then paging behavior. No filler, though the filter enumeration in the second sentence is largely redundant with the schema the agent will already read.
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 needn't be re-explained, and annotations cover safety. Still, for a 14-parameter search tool with an overlapping sibling search tool, the description never addresses which search tool to pick or the result-set ceiling, leaving that routing and limit information to be discovered elsewhere.
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 14 parameters, including enums, defaults, bounds, and rejection rules for blank/whitespace values. The description merely restates categories of filters (author, journal, MeSH, language, species, free full text) without adding syntax or semantics beyond the schema, which is the expected baseline.
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 PubMed') and enumerates the capability surface: full query syntax, filters, date ranges, and return of PMIDs/summaries. It does not, however, distinguish itself from the sibling pubmed_europepmc_search, which is also a literature search tool, so an agent gets no in-description routing signal.
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 mention of offset for 'paging through large result sets' hints at large-retrieval scenarios, and the summaryCount semantics (carried in the schema, not the description) imply handing leftover PMIDs to pubmed_fetch_articles. There is no explicit when-to-use-this-vs-europepmc_search guidance or any stated exclusion.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
pubmed_spell_checkPubmed Spell CheckARead-onlyInspect
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 — every misspelled token is corrected in one call (alzhiemer diseese treatmnt outcomse → alzheimer disease treatment outcomes), and hasSuggestion is false when NCBI has no change to offer. 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. |
Output Schema
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| original | No | Original query |
| corrected | No | Corrected query (same as original if no suggestion) |
| hasSuggestion | No | Whether NCBI suggested a correction |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint and openWorldHint, so safety is covered. The description adds real behavior beyond that: all misspelled tokens are fixed in a single call, and hasSuggestion is false when NCBI offers no change — a non-obvious edge case. It omits any mention of external-service latency or rate limits, keeping it short of a 5.
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 purpose, then trigger conditions, then a compact example, then the follow-up action. Dense but every clause carries information; no 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?
An output schema exists, and the description still names the key return fields (corrected, hasSuggestion) and their meaning, so the agent knows exactly how to branch on the result. With one fully documented parameter and annotations covering safety, nothing needed 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 single parameter already documents minLength and the whitespace/zero-width-space rejection rule. The description's concrete example ('alzhiemer diseese treatmnt outcomse' → 'alzheimer disease treatment outcomes') illustrates effect but adds no syntax or constraint detail the schema lacks, 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?
States a specific verb+resource ('Spell-check a PubMed search query') plus the upstream service (NCBI ESpell) and the return ('get the corrected query back'). It is immediately distinguishable from siblings like pubmed_search_articles, which are referenced by name as the tool it complements.
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 explicit triggers: 'after a zero-hit or thin pubmed_search_articles result, or when a drug, gene, disease, or author name may be misspelled.' It also closes the loop by telling the agent to 'Re-run the search with corrected,' so the workflow around the sibling is fully specified.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Tool Schema Changelog
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
10 tool updates
v2.10.19- Changed
pubmed_convert_ids2 fields changed- changed
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). `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." - changed
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" +]
- Changed
pubmed_europepmc_fetch1 field changed- changed
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). `europepmc_disabled`: Europe PMC service is disabled via EUROPEPMC_ENABLED=false. Other values are possible when a failure originates below the handler."
- Changed
pubmed_europepmc_search4 fields changed- changed
Input 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." - changed
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." - changed
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." - changed
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" +]
- Changed
pubmed_fetch_articles3 fields changed- added
Output 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" +} - changed
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." - changed
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" +]
- Changed
pubmed_fetch_fulltext2 fields changed- changed
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." - changed
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" +]
- Changed
pubmed_format_citations2 fields changed- changed
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." - changed
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" +]
- Changed
pubmed_lookup_citation8 fields changed- removed
Input 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" - } -] - changed
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." - added
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" +} - added
Input schema / properties / citations / maxItemsAdded value: +25 - added
Input schema / properties / citations / minItemsAdded value: +1 - added
Input schema / properties / citations / typeAdded value: +"array" - changed
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." - changed
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" +]
- Changed
pubmed_lookup_mesh3 fields changed- changed
Input 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." - changed
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." - changed
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" +]
- Changed
pubmed_search_articles11 fields changed- changed
Input 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." - changed
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." - changed
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." - changed
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." - changed
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." - changed
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." - changed
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." - changed
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." - changed
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." - changed
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." - changed
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" +]
- Changed
pubmed_spell_check3 fields changed- changed
Input 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." - changed
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." - changed
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" +]
11 tool updates
v2.10.18- Changed
pubmed_convert_ids1 field changed- changed
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). `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."
- Changed
pubmed_europepmc_fetch1 field changed- changed
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."
- Changed
pubmed_europepmc_search4 fields changed- changed
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 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." - changed
Input 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." - changed
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" + ] + } +] - changed
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."
- Changed
pubmed_fetch_articles1 field changed- changed
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). `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."
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pubmed_fetch_fulltext10 fields changed- changed
Input 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." - changed
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." - changed
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" + } +] - changed
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). `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). Other values are possible when a failure originates below the handler." - changed
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" +] - changed
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." - added
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" +} - changed
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." - added
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" +} - changed
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."
- Changed
pubmed_find_related2 fields changed- changed
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). `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." - changed
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" +]
- Changed
pubmed_format_citations1 field changed- changed
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`: 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."
- Changed
pubmed_lookup_citation7 fields changed- added
Input 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]*$", + "type": "string" + } + }, + "type": "object" + } +] - changed
Input schema / properties / citations / descriptionPrevious value: -"Citations to look up. More fields = better match accuracy."New value: +"Citations to look up — an array of up to 25, or a single citation object. More fields = better match accuracy." - removed
Input schema / properties / citations / itemsRemoved value: -{ - "description": "Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.", - "properties": { - "authorName": { - "description": "Author name, typically \"lastname initials\" (e.g., \"mann bj\"). Cannot contain a pipe (\"|\") or a line break.", - "pattern": "^[^|\\r\\n]*$", - "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" -} - removed
Input schema / properties / citations / maxItemsRemoved value: -25 - removed
Input schema / properties / citations / minItemsRemoved value: -1 - removed
Input schema / properties / citations / typeRemoved value: -"array" - changed
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`: 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."
- Changed
pubmed_lookup_mesh1 field changed- changed
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). `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."
- Changed
pubmed_search_articles3 fields changed- changed
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 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." - changed
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" + ] + } +] - changed
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). `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."
- Changed
pubmed_spell_check1 field changed- changed
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). `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."
9 tool updates
v2.10.12- Changed
pubmed_convert_ids3 fields changed- changed
Input 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." - changed
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." - changed
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" +]
- Changed
pubmed_fetch_articles9 fields changed- changed
Output 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." - added
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" +} - changed
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)" - added
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" +} - added
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" +} - added
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" +} - changed
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`." - added
Output schema / properties / articles / items / requiredAdded value: +[ + "recordType" +] - changed
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."
- Changed
pubmed_fetch_fulltext19 fields changed- changed
Input 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." - removed
Input schema / properties / dois / items / minLengthRemoved value: -3 - added
Input schema / properties / dois / items / patternAdded value: +"^10\\.[^\\s,]+\\/[^\\s,]+$" - added
Input 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" +} - added
Input 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" +} - changed
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 — 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." - changed
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 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." - changed
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" + }, + "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" + } +] - changed
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." - added
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" +} - added
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" +} - added
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" +} - added
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" +} - added
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" +} - added
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" +} - changed
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." - changed
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" +] - changed
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." - changed
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" +]
- Changed
pubmed_find_related9 fields changed- changed
Output 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`." - added
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" +} - added
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" +} - added
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" +} - added
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" +} - changed
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." - added
Output 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" +} - changed
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." - changed
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."
- Changed
pubmed_format_citations1 field changed- changed
Output 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."
- Changed
pubmed_lookup_citation11 fields changed- changed
Input 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." - added
Input schema / properties / citations / items / properties / authorName / patternAdded value: +"^[^|\\r\\n]*$" - changed
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." - added
Input schema / properties / citations / items / properties / firstPage / patternAdded value: +"^[^|\\r\\n]*$" - changed
Input schema / properties / citations / items / properties / journal / descriptionPrevious value: -"Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\")"New value: +"Journal title or ISO abbreviation (e.g., \"proc natl acad sci u s a\"). Cannot contain a pipe (\"|\") or a line break." - added
Input schema / properties / citations / items / properties / journal / patternAdded value: +"^[^|\\r\\n]*$" - changed
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." - changed
Input schema / properties / citations / items / properties / volume / descriptionPrevious value: -"Volume number"New value: +"Volume number. Cannot contain a pipe (\"|\") or a line break." - added
Input schema / properties / citations / items / properties / volume / patternAdded value: +"^[^|\\r\\n]*$" - changed
Input schema / properties / citations / items / properties / year / descriptionPrevious value: -"Publication year (e.g., \"1991\")"New value: +"Publication year (e.g., \"1991\"). Cannot contain a pipe (\"|\") or a line break." - added
Input schema / properties / citations / items / properties / year / patternAdded value: +"^[^|\\r\\n]*$"
- Changed
pubmed_lookup_mesh3 fields changed- changed
Input 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." - changed
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." - changed
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" +]
- Changed
pubmed_search_articles9 fields changed- changed
Input 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." - changed
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." - changed
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" +] - changed
Output 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`." - added
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" +} - added
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" +} - added
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" +} - added
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" +} - changed
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."
- Changed
pubmed_spell_check3 fields changed- changed
Input 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." - changed
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." - changed
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" +]
5 tool updates
v2.10.8- Changed
pubmed_europepmc_fetch3 fields changed- changed
Output 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." - changed
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." - changed
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."
- Changed
pubmed_europepmc_search3 fields changed- changed
Output 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." - changed
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." - changed
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."
- Changed
pubmed_fetch_articles6 fields changed- added
Input 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" +} - added
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" +} - changed
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." - changed
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." - added
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" +} - changed
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."
- Changed
pubmed_fetch_fulltext10 fields changed- changed
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. 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." - added
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" +} - changed
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", - "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" + } +] - added
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" +} - changed
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." - changed
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." - changed
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`." - changed
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." - changed
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." - added
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" +}
- Changed
pubmed_find_related4 fields changed- changed
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). `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." - changed
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" +] - changed
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." - changed
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."
11 tool updates
v2.10.4- Changed
pubmed_convert_ids6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "records", + "totalConverted", + "totalSubmitted" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "records", - "totalConverted", - "totalSubmitted" -]
- Changed
pubmed_europepmc_fetch6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "records" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "records" -]
- Changed
pubmed_europepmc_search6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "hits", + "cursorMark", + "searchUrl", + "query", + "totalCount", + "appliedSources" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "hits", - "cursorMark", - "searchUrl", - "query", - "totalCount", - "appliedSources" -]
- Changed
pubmed_fetch_articles6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "articles", + "totalReturned" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "articles", - "totalReturned" -]
- Changed
pubmed_fetch_fulltext7 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "articles", + "totalReturned" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "articles", - "totalReturned" -]
- Changed
pubmed_find_related6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "sourcePmid", + "relationship", + "offset", + "articles", + "totalCount", + "source" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "sourcePmid", - "relationship", - "offset", - "articles", - "totalCount", - "source" -]
- Changed
pubmed_format_citations6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "citations", + "totalSubmitted", + "totalFormatted" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "citations", - "totalSubmitted", - "totalFormatted" -]
- Changed
pubmed_lookup_citation6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "results", + "totalMatched", + "totalSubmitted", + "totalWarnings" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "results", - "totalMatched", - "totalSubmitted", - "totalWarnings" -]
- Changed
pubmed_lookup_mesh6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "query", + "offset", + "results", + "totalCount" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "query", - "offset", - "results", - "totalCount" -]
- Changed
pubmed_search_articles6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "query", + "offset", + "pmids", + "summaries", + "searchUrl", + "effectiveQuery", + "totalCount", + "appliedFilters" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "query", - "offset", - "pmids", - "summaries", - "searchUrl", - "effectiveQuery", - "totalCount", - "appliedFilters" -]
- Changed
pubmed_spell_check6 fields changed- changed
Input schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Input schema / additionalPropertiesAdded value: +false - changed
Output schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema" - added
Output schema / anyOfAdded value: +[ + { + "not": { + "required": [ + "error" + ] + }, + "required": [ + "original", + "corrected", + "hasSuggestion" + ] + }, + { + "required": [ + "error" + ] + } +] - added
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" +} - removed
Output schema / requiredRemoved value: -[ - "original", - "corrected", - "hasSuggestion" -]
7 tool updates
v2.10.2- Changed
pubmed_convert_ids1 field changed- changed
Output schema / properties / records / items / properties / doi / descriptionPrevious value: -"Digital Object Identifier; absent if no DOI is on record"New value: +"Digital Object Identifier, cased as the PMC ID Converter reports it; absent if no DOI is on record. DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ from a Europe PMC-sourced `doi` — compare the two case-insensitively."
- Added
pubmed_europepmc_fetch - Changed
pubmed_europepmc_search5 fields changed- changed
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`. 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 combined with `AND SRC:` must be unquoted — the quoted form matches nothing. Free text is matched broadly across abstract/title/keywords." - changed
Output schema / properties / hits / items / properties / abstractSnippet / descriptionPrevious value: -"First few hundred characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when `resultType: \"core\"` is requested"New value: +"First 400 characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when `resultType: \"core\"` is requested, with a trailing … appended when the abstract was cut. Check `abstractTruncated` before treating it as the whole abstract." - added
Output schema / properties / hits / items / properties / abstractTruncatedAdded value: +{ + "description": "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.", + "type": "boolean" +} - changed
Output schema / properties / hits / items / properties / doi / descriptionPrevious value: -"DOI when present"New value: +"DOI when present, cased as Europe PMC reports it. DOIs are case-insensitive by spec and no case normalization is applied here, so the same DOI can arrive in a different case from `pubmed_fetch_articles` (Europe PMC `10.1056/nejmoa2212948`, NCBI `10.1056/NEJMoa2212948`) — a byte-for-byte comparison across the two reports a false mismatch." - changed
Output schema / properties / hits / items / properties / epmcId / descriptionPrevious value: -"Europe PMC's internal record id; key for `fullTextXML` lookup"New 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."
- Changed
pubmed_fetch_articles1 field changed- changed
Output schema / properties / articles / items / properties / doi / descriptionPrevious value: -"DOI"New value: +"DOI, cased as NCBI reports it (usually the publisher's mixed case). DOIs are case-insensitive by spec and no case normalization is applied here, so the same DOI can arrive in a different case from `pubmed_europepmc_search` and `pubmed_europepmc_fetch` (NCBI `10.1056/NEJMoa2212948`, Europe PMC `10.1056/nejmoa2212948`) — a byte-for-byte comparison across the two reports a false mismatch."
- Changed
pubmed_fetch_fulltext11 fields changed- added
Input schema / properties / maxCharactersAdded value: +{ + "description": "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.", + "maximum": 1000000, + "minimum": 1, + "type": "integer" +} - added
Input schema / properties / maxCharactersPerSectionAdded value: +{ + "description": "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.", + "maximum": 1000000, + "minimum": 1, + "type": "integer" +} - added
Input schema / properties / overflowModeAdded value: +{ + "default": "truncate", + "description": "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.", + "enum": [ + "truncate", + "outline" + ], + "type": "string" +} - changed
Input schema / properties / pmcids / descriptionPrevious value: -"PMC IDs to fetch (e.g. [\"PMC9575052\"]). Provide exactly one of `pmcids`, `pmids`, or `dois`."New 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." - changed
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", - "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" - }, - "pmid": { - "description": "PubMed ID when input was `pmids`; absent for `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", + "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" + } +] - changed
Output schema / properties / notice / descriptionPrevious value: -"Optional guidance when a `sections` filter removed every body section — names the requested section terms and the affected article id(s), and suggests retrying without `sections` or using broader headings. Absent when no section filter was applied or sections matched."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`. Absent when none of those applies." - added
Output schema / properties / truncationAdded value: +{ + "additionalProperties": false, + "description": "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.", + "properties": { + "articles": { + "description": "Per-article accounting, covering only the articles the budget shortened", + "items": { + "additionalProperties": false, + "description": "Character accounting for one article the budget shortened", + "properties": { + "id": { + "description": "Identifier for the article — PMCID, PMID, DOI, or Europe PMC id, whichever the article carries first", + "type": "string" + }, + "originalCharacters": { + "description": "Body characters this article carried before the budget pass", + "type": "number" + }, + "returnedCharacters": { + "description": "Body characters this article carries in the response", + "type": "number" + }, + "sections": { + "description": "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.", + "items": { + "additionalProperties": false, + "description": "Character accounting for one body section of a budgeted article", + "properties": { + "originalCharacters": { + "description": "Body characters this section carried before the budget pass", + "type": "number" + }, + "returnedCharacters": { + "description": "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.", + "type": "number" + }, + "title": { + "description": "Section heading, when the section carries one", + "type": "string" + }, + "truncated": { + "description": "True when the section returned fewer characters than it originally carried", + "type": "boolean" + } + }, + "required": [ + "originalCharacters", + "returnedCharacters", + "truncated" + ], + "type": "object" + }, + "type": "array" + }, + "source": { + "description": "Which output shape was budgeted: `pmc` budgets body sections and subsections, `unpaywall` budgets the single `content` body", + "enum": [ + "pmc", + "unpaywall" + ], + "type": "string" + } + }, + "required": [ + "id", + "source", + "originalCharacters", + "returnedCharacters" + ], + "type": "object" + }, + "type": "array" + }, + "maxCharacters": { + "description": "The `maxCharacters` budget applied, when set", + "type": "number" + }, + "maxCharactersPerSection": { + "description": "The `maxCharactersPerSection` budget applied, when set", + "type": "number" + }, + "mode": { + "description": "The `overflowMode` that produced these results", + "enum": [ + "truncate", + "outline" + ], + "type": "string" + }, + "omittedSections": { + "description": "Body sections dropped entirely because an article budget was exhausted before reaching them. Always 0 in `outline` mode, which keeps every heading.", + "type": "number" + }, + "originalCharacters": { + "description": "Body characters the shortened articles carried before the budget pass", + "type": "number" + }, + "returnedCharacters": { + "description": "Body characters the shortened articles carry in this response", + "type": "number" + } + }, + "required": [ + "mode", + "originalCharacters", + "returnedCharacters", + "omittedSections", + "articles" + ], + "type": "object" +} - changed
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-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. 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)." - changed
Output schema / properties / unavailable / items / properties / reason / enumPrevious value: -[ - "not-found", - "no-pmc-fallback-disabled", - "no-epmc-fulltext", - "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", + "no-oa", + "fetch-failed", + "parse-failed", + "service-error" +] - changed
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-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: 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." - changed
Output schema / properties / unavailable / items / properties / triedTiers / items / properties / outcome / enumPrevious value: -[ - "not-attempted", - "miss", - "no-fulltext", - "no-doi", - "no-oa", - "fetch-failed", - "parse-failed", - "service-error" -]New value: +[ + "not-attempted", + "miss", + "no-fulltext", + "no-body", + "no-doi", + "no-oa", + "fetch-failed", + "parse-failed", + "service-error" +]
- Changed
pubmed_lookup_mesh6 fields changed- added
Input schema / properties / offsetAdded value: +{ + "default": 0, + "description": "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.", + "maximum": 9007199254740991, + "minimum": 0, + "type": "integer" +} - added
Output schema / properties / nextOffsetAdded value: +{ + "description": "Offset to request for the next page. Omitted when this is the last page, so its absence is the end-of-results signal.", + "type": "number" +} - changed
Output schema / properties / notice / descriptionPrevious value: -"Optional guidance when no descriptors matched — suggests spell-check or free-text search. Absent on successful results."New value: +"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." - added
Output schema / properties / offsetAdded value: +{ + "description": "Result offset this page was read from", + "type": "number" +} - changed
Output schema / properties / totalCount / descriptionPrevious value: -"Total matching MeSH descriptors"New value: +"Total MeSH descriptors matching the query upstream, before the maxResults cap" - changed
Output schema / requiredPrevious value: -[ - "query", - "results", - "totalCount" -]New value: +[ + "query", + "offset", + "results", + "totalCount" +]
- Changed
pubmed_search_articles5 fields changed- changed
Input schema / properties / offset / descriptionPrevious value: -"Result offset for pagination (0-based)"New value: +"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." - changed
Input schema / properties / offset / maximumPrevious value: -9007199254740991New value: +9998 - changed
Input schema / properties / summaryCount / descriptionPrevious value: -"Fetch brief summaries for top N results (0 = PMIDs only)"New value: +"Fetch brief summaries for top N results (0 = PMIDs only). Above the 50 cap, pass the remaining PMIDs to pubmed_fetch_articles." - changed
Output schema / properties / notice / descriptionPrevious value: -"Optional guidance when results are empty or paging overshot — e.g. how to broaden filters or reset offset. Absent on successful result pages."New value: +"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." - changed
Output schema / properties / summaries / items / properties / doi / descriptionPrevious value: -"DOI"New value: +"DOI, cased as NCBI reports it. DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ from a Europe PMC-sourced `doi` — compare the two case-insensitively."
1 tool update
v2.9.8- Changed
pubmed_fetch_fulltext1 field changed- added
Output schema / properties / noticeAdded value: +{ + "description": "Optional guidance when a `sections` filter removed every body section — names the requested section terms and the affected article id(s), and suggests retrying without `sections` or using broader headings. Absent when no section filter was applied or sections matched.", + "type": "string" +}
3 tool updates
v2.9.6- Changed
pubmed_convert_ids1 field changed- changed
Input 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\"."New 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)."
- Changed
pubmed_europepmc_search1 field changed- changed
Output schema / properties / hits / items / properties / abstractSnippet / descriptionPrevious value: -"First few hundred characters of the abstract when `resultType: \"core\"` is requested"New value: +"First few hundred characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when `resultType: \"core\"` is requested"
- Changed
pubmed_lookup_mesh4 fields changed- added
Output schema / properties / results / items / properties / entrezUidAdded value: +{ + "description": "NCBI Entrez UID for this record — the join key for E-utilities (eSummary/eFetch db=mesh).", + "type": "string" +} - changed
Output schema / properties / results / items / properties / meshId / descriptionPrevious value: -"MeSH descriptor unique identifier"New 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." - changed
Output schema / properties / results / items / properties / treeNumbers / descriptionPrevious value: -"MeSH tree numbers"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." - changed
Output schema / properties / results / items / requiredPrevious value: -[ - "meshId", - "name" -]New value: +[ + "meshId", + "entrezUid", + "name" +]
4 tool updates
v2.9.4- Changed
pubmed_europepmc_search3 fields changed- removed
Output schema / properties / hitCountRemoved value: -{ - "description": "Total matching records across all pages", - "type": "number" -} - added
Output schema / properties / totalCountAdded value: +{ + "description": "Total matching records across all pages", + "type": "number" +} - changed
Output schema / requiredPrevious value: -[ - "hits", - "cursorMark", - "searchUrl", - "query", - "hitCount", - "appliedSources" -]New value: +[ + "hits", + "cursorMark", + "searchUrl", + "query", + "totalCount", + "appliedSources" +]
- Changed
pubmed_find_related3 fields changed- added
Output schema / properties / totalCountAdded value: +{ + "description": "Total related articles found before windowing", + "type": "number" +} - removed
Output schema / properties / totalFoundRemoved value: -{ - "description": "Total related articles found before windowing", - "type": "number" -} - changed
Output schema / requiredPrevious value: -[ - "sourcePmid", - "relationship", - "offset", - "articles", - "totalFound", - "source" -]New value: +[ + "sourcePmid", + "relationship", + "offset", + "articles", + "totalCount", + "source" +]
- Changed
pubmed_lookup_mesh2 fields changed- added
Output schema / properties / totalCountAdded value: +{ + "description": "Total matching MeSH descriptors", + "type": "number" +} - changed
Output schema / requiredPrevious value: -[ - "query", - "results" -]New value: +[ + "query", + "results", + "totalCount" +]
- Changed
pubmed_search_articles3 fields changed- added
Output schema / properties / totalCountAdded value: +{ + "description": "Total matching articles", + "type": "number" +} - removed
Output schema / properties / totalFoundRemoved value: -{ - "description": "Total matching articles", - "type": "number" -} - changed
Output schema / requiredPrevious value: -[ - "query", - "offset", - "pmids", - "summaries", - "searchUrl", - "effectiveQuery", - "totalFound", - "appliedFilters" -]New value: +[ + "query", + "offset", + "pmids", + "summaries", + "searchUrl", + "effectiveQuery", + "totalCount", + "appliedFilters" +]
6 tool updates
v2.9.1- Changed
pubmed_europepmc_search1 field changed- changed
Input 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."New 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."
- Changed
pubmed_fetch_articles1 field changed- added
Output schema / properties / noticeAdded value: +{ + "description": "Optional guidance when no articles were returned — points to discovery tools. Absent on successful fetches.", + "type": "string" +}
- Changed
pubmed_fetch_fulltext1 field changed- changed
Input 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`. Covers preprints and EPMC-only OA records that lack PMID/PMCID. Chain: Europe PMC search-by-DOI → fullTextXML → Unpaywall."New 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."
- Changed
pubmed_find_related6 fields changed- added
Input schema / properties / offsetAdded value: +{ + "default": 0, + "description": "Result offset for pagination (0-based); page through results by incrementing by maxResults", + "maximum": 9007199254740991, + "minimum": 0, + "type": "integer" +} - changed
Output schema / properties / notice / descriptionPrevious value: -"Optional guidance when results are empty — e.g. invalid source PMID, or references requested for a non-PMC source. Absent on successful result pages."New value: +"Guidance when results are empty, a fallback provider answered, or offset overshot. Absent on a clean NCBI result page." - added
Output schema / properties / offsetAdded value: +{ + "description": "Result offset used", + "type": "number" +} - added
Output schema / properties / sourceAdded value: +{ + "description": "Provider that answered this request", + "enum": [ + "ncbi", + "europepmc", + "openalex" + ], + "type": "string" +} - changed
Output schema / properties / totalFound / descriptionPrevious value: -"Total related articles found before truncation"New value: +"Total related articles found before windowing" - changed
Output schema / requiredPrevious value: -[ - "sourcePmid", - "relationship", - "articles", - "totalFound" -]New value: +[ + "sourcePmid", + "relationship", + "offset", + "articles", + "totalFound", + "source" +]
- Changed
pubmed_format_citations3 fields changed- changed
Input schema / properties / format / anyOfPrevious value: -[ - { - "description": "Single citation style. One of: apa, mla, bibtex, ris.", - "enum": [ - "apa", - "mla", - "bibtex", - "ris" - ], - "type": "string" - }, - { - "description": "Multiple citation styles to generate. Each entry: apa, mla, bibtex, or ris.", - "items": { - "enum": [ - "apa", - "mla", - "bibtex", - "ris" - ], - "type": "string" - }, - "minItems": 1, - "type": "array" - } -]New value: +[ + { + "description": "Single citation style. One of: apa, mla, bibtex, ris, vancouver.", + "enum": [ + "apa", + "mla", + "bibtex", + "ris", + "vancouver" + ], + "type": "string" + }, + { + "description": "Multiple citation styles to generate. Each entry: apa, mla, bibtex, ris, or vancouver.", + "items": { + "enum": [ + "apa", + "mla", + "bibtex", + "ris", + "vancouver" + ], + "type": "string" + }, + "minItems": 1, + "type": "array" + } +] - changed
Input schema / properties / format / descriptionPrevious value: -"Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris."New value: +"Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris, vancouver." - added
Output schema / properties / noticeAdded value: +{ + "description": "Optional guidance when no citations were produced — points to discovery tools. Absent when at least one citation was produced.", + "type": "string" +}
- Changed
pubmed_lookup_citation1 field changed- changed
Input schema / properties / citations / items / descriptionPrevious value: -"Citation to match against PubMed. Must include at least one bibliographic field (journal, year, volume, firstPage, or authorName)."New 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."
2 tool updates
v2.7.8- Changed
pubmed_europepmc_search1 field changed- changed
Output schema / requiredPrevious value: -[ - "query", - "hits", - "hitCount", - "cursorMark", - "appliedSources", - "searchUrl" -]New value: +[ + "hits", + "cursorMark", + "searchUrl", + "query", + "hitCount", + "appliedSources" +]
- Changed
pubmed_search_articles1 field changed- changed
Output schema / requiredPrevious value: -[ - "query", - "effectiveQuery", - "appliedFilters", - "totalFound", - "offset", - "pmids", - "summaries", - "searchUrl" -]New value: +[ + "query", + "offset", + "pmids", + "summaries", + "searchUrl", + "effectiveQuery", + "totalFound", + "appliedFilters" +]
10 tool updates
v2.7.6- Added
pubmed_convert_ids - Added
pubmed_europepmc_search - Added
pubmed_fetch_articles - Added
pubmed_fetch_fulltext - Added
pubmed_find_related - Added
pubmed_format_citations - Added
pubmed_lookup_citation - Added
pubmed_lookup_mesh - Added
pubmed_search_articles - Added
pubmed_spell_check
9 tool updates
v2.7.4- Removed
pubmed_convert_ids - Removed
pubmed_fetch_articles - Removed
pubmed_fetch_fulltext - Removed
pubmed_find_related - Removed
pubmed_format_citations - Removed
pubmed_lookup_citation - Removed
pubmed_lookup_mesh - Removed
pubmed_search_articles - Removed
pubmed_spell_check
13 tool updates
v2.3.2- Removed
pubmed_article_connections - Added
pubmed_convert_ids - Added
pubmed_fetch_articles - Removed
pubmed_fetch_contents - Added
pubmed_fetch_fulltext - Added
pubmed_find_related - Added
pubmed_format_citations - Removed
pubmed_generate_chart - Added
pubmed_lookup_citation - Added
pubmed_lookup_mesh - Removed
pubmed_research_agent - Changed
pubmed_search_articles30 fields changed- removed
Input schema / additionalPropertiesRemoved value: -false - added
Input schema / properties / authorAdded value: +{ + "description": "Filter by author name (e.g. \"Smith J\")", + "type": "string" +} - removed
Input schema / properties / dateRange / additionalPropertiesRemoved value: -false - changed
Input schema / properties / dateRange / descriptionPrevious value: -"Defines an optional date range for the search."New value: +"Filter by date range" - changed
Input schema / properties / dateRange / properties / dateType / descriptionPrevious value: -"The type of date to filter by: 'pdat' (Publication Date), 'mdat' (Modification Date), 'edat' (Entrez Date). Default is 'pdat'."New value: +"Date type: pdat (publication), mdat (modification), edat (entrez)" - changed
Input schema / properties / dateRange / properties / maxDate / descriptionPrevious value: -"The end date for the search range (YYYY, YYYY/MM, or YYYY/MM/DD)."New value: +"End date (YYYY/MM/DD, YYYY/MM, or YYYY)" - removed
Input schema / properties / dateRange / properties / maxDate / patternRemoved value: -"^\\d{4}(\\/\\d{2}(\\/\\d{2})?)?$" - changed
Input schema / properties / dateRange / properties / minDate / descriptionPrevious value: -"The start date for the search range (YYYY, YYYY/MM, or YYYY/MM/DD)."New value: +"Start date (YYYY/MM/DD, YYYY/MM, or YYYY)" - removed
Input schema / properties / dateRange / properties / minDate / patternRemoved value: -"^\\d{4}(\\/\\d{2}(\\/\\d{2})?)?$" - added
Input schema / properties / dateRange / requiredAdded value: +[ + "minDate", + "maxDate" +] - removed
Input schema / properties / fetchBriefSummariesRemoved value: -{ - "default": 0, - "description": "Number of top PMIDs for which to fetch brief summaries using ESummary. Set to 0 to disable. Max 50. Default 0.", - "maximum": 50, - "minimum": 0, - "type": "integer" -} - removed
Input schema / properties / filterByPublicationTypesRemoved value: -{ - "description": "An array of publication types to filter by (e.g., [\"Review\", \"Clinical Trial\"]).", - "items": { - "type": "string" - }, - "type": "array" -} - added
Input schema / properties / freeFullTextAdded value: +{ + "description": "Only include free full text articles", + "type": "boolean" +} - added
Input schema / properties / hasAbstractAdded value: +{ + "description": "Only include articles with abstracts", + "type": "boolean" +} - added
Input schema / properties / journalAdded value: +{ + "description": "Filter by journal name", + "type": "string" +} - added
Input schema / properties / languageAdded value: +{ + "description": "Filter by language (e.g. \"english\")", + "type": "string" +} - changed
Input schema / properties / maxResults / descriptionPrevious value: -"Maximum number of articles to retrieve. Corresponds to ESearch's 'retmax' parameter. Default is 20, max is 1000."New value: +"Maximum results to return" - removed
Input schema / properties / maxResults / exclusiveMinimumRemoved value: -0 - added
Input schema / properties / maxResults / minimumAdded value: +1 - added
Input schema / properties / meshTermsAdded value: +{ + "description": "Filter by MeSH terms", + "items": { + "type": "string" + }, + "type": "array" +} - added
Input schema / properties / offsetAdded value: +{ + "default": 0, + "description": "Result offset for pagination (0-based)", + "maximum": 9007199254740991, + "minimum": 0, + "type": "integer" +} - added
Input schema / properties / publicationTypesAdded value: +{ + "description": "Filter by publication type (e.g. \"Review\", \"Clinical Trial\", \"Meta-Analysis\")", + "items": { + "type": "string" + }, + "type": "array" +} - added
Input schema / properties / queryAdded value: +{ + "description": "PubMed search query (supports full NCBI syntax)", + "minLength": 1, + "type": "string" +} - removed
Input schema / properties / queryTermRemoved value: -{ - "description": "The primary keyword or phrase to search for in PubMed. Must be at least 3 characters long.", - "minLength": 3, - "type": "string" -} - added
Input schema / properties / sortAdded value: +{ + "default": "relevance", + "description": "Sort order: relevance (default), pub_date (newest first), author, or journal", + "enum": [ + "relevance", + "pub_date", + "author", + "journal" + ], + "type": "string" +} - removed
Input schema / properties / sortByRemoved value: -{ - "default": "relevance", - "description": "Sorting criteria for results. Options: 'relevance' (default), 'pub_date', 'author', 'journal_name'.", - "enum": [ - "relevance", - "pub_date", - "author", - "journal_name" - ], - "type": "string" -} - added
Input schema / properties / speciesAdded value: +{ + "description": "Filter by species", + "enum": [ + "humans", + "animals" + ], + "type": "string" +} - added
Input schema / properties / summaryCountAdded value: +{ + "default": 0, + "description": "Fetch brief summaries for top N results (0 = PMIDs only)", + "maximum": 50, + "minimum": 0, + "type": "integer" +} - changed
Input schema / requiredPrevious value: -[ - "queryTerm" -]New value: +[ + "query" +] - changed
Output schema / (root)Previous value: -nullNew value: +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "additionalProperties": false, + "properties": { + "offset": { + "description": "Result offset used", + "type": "number" + }, + "pmids": { + "description": "PubMed IDs", + "items": { + "type": "string" + }, + "type": "array" + }, + "query": { + "description": "Original query", + "type": "string" + }, + "searchUrl": { + "description": "PubMed search URL", + "type": "string" + }, + "summaries": { + "description": "Brief summaries (empty array when summaryCount is 0)", + "items": { + "additionalProperties": false, + "properties": { + "authors": { + "description": "Formatted author string", + "type": "string" + }, + "doi": { + "description": "DOI", + "type": "string" + }, + "pmcId": { + "description": "PMC ID", + "type": "string" + }, + "pmcUrl": { + "description": "PMC URL", + "type": "string" + }, + "pmid": { + "description": "PubMed ID", + "type": "string" + }, + "pubDate": { + "description": "Publication date", + "type": "string" + }, + "pubmedUrl": { + "description": "PubMed URL", + "type": "string" + }, + "source": { + "description": "Journal source", + "type": "string" + }, + "title": { + "description": "Article title", + "type": "string" + } + }, + "required": [ + "pmid" + ], + "type": "object" + }, + "type": "array" + }, + "totalFound": { + "description": "Total matching articles", + "type": "number" + } + }, + "required": [ + "query", + "totalFound", + "offset", + "pmids", + "summaries", + "searchUrl" + ], + "type": "object" +}
- Added
pubmed_spell_check
5 tool updates
v1.0.0- First observed
pubmed_article_connections - First observed
pubmed_fetch_contents - First observed
pubmed_generate_chart - First observed
pubmed_research_agent - First observed
pubmed_search_articles
TDQS
Scored across 11 tools
Each tool generally maps to a clear action/resource pairing, especially search vs. fetch vs. formatting vs. lookups. The main mild risk is choosing between pubmed_search_articles and pubmed_europepmc_search, since they retrieve overlapping literatures even though the latter targets extended preprints/OA/PAT/AGR coverage.
All tools share the pubmed_ namespace and broadly readable names. Ordering varies slightly, notably pubmed_europepmc_search placing the service qualifier before the action compared with verb-first names elsewhere.
Eleven tools fit well within the recommended 3–15 range and correspond to genuinely useful stages of biomedical literature research without filler.
The surface covers literature search/discovery, metadata and full-text retrieval, ID mapping, citation formatting, spelling repair, MeSH browsing, and related-article traversal. Possible omissions involve richer personal-library/workflow integrations such as alerts or saved-search handling, but standard researcher needs are largely met.
Maintenance
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