npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.4.1 → 2.5.0 - Mend

@cyanheads/pubmed-mcp-server 2.4.1 → 2.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (37) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.4.1
+**Version:** 2.5.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -221,6 +221,7 @@ Available skills:
 | `setup` | Post-init project orientation |
 | `design-mcp-server` | Design tool surface, resources, and services for a new server |
 | `add-tool` | Scaffold a new tool definition |
+| `add-app-tool` | Scaffold an MCP App tool + paired UI resource |
 | `add-resource` | Scaffold a new resource definition |
 | `add-prompt` | Scaffold a new prompt definition |
 | `add-service` | Scaffold a new service integration |
@@ -228,11 +229,12 @@ Available skills:
 | `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
 | `devcheck` | Lint, format, typecheck, audit |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
-| `maintenance` | Sync skills and dependencies after updates |
+| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills after `bun update --latest` |
 | `api-auth` | Auth modes, scopes, JWT/OAuth |
 | `api-config` | AppConfig, parseConfig, env vars |
 | `api-context` | Context interface, logger, state, progress |
 | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
+| `api-linter` | Definition lint rules reference (`format-parity`, `schema-*`, `server-json-*`, …) |
 | `api-services` | LLM, Speech, Graph services |
 | `api-testing` | createMockContext, test patterns |
 | `api-utils` | Formatting, parsing, security, pagination, scheduling |

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.4.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
+[![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.5.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
 [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)

package/dist/index.js CHANGED Viewed

@@ -30,6 +30,28 @@ await createApp({
     ],
     resources: [databaseInfoResource],
     prompts: [researchPlanPrompt],
+    landing: {
+        tagline: 'Search PubMed, fetch articles, generate citations, explore MeSH terms, and discover related research.',
+        repoRoot: 'https://github.com/cyanheads/pubmed-mcp-server',
+        links: [
+            { label: 'PubMed', href: 'https://pubmed.ncbi.nlm.nih.gov/', external: true },
+            {
+                label: 'E-utilities docs',
+                href: 'https://www.ncbi.nlm.nih.gov/books/NBK25501/',
+                external: true,
+            },
+            {
+                label: 'Get an NCBI API key',
+                href: 'https://www.ncbi.nlm.nih.gov/account/settings/',
+                external: true,
+            },
+            { label: 'MeSH Browser', href: 'https://meshb.nlm.nih.gov/', external: true },
+        ],
+        envExample: {
+            NCBI_API_KEY: 'your-ncbi-api-key',
+            NCBI_ADMIN_EMAIL: 'you@example.com',
+        },
+    },
     setup() {
         initNcbiService();
     },

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/_concepts.d.ts ADDED Viewed

@@ -0,0 +1,41 @@
+/**
+ * @fileoverview Ontology-backed semantic concept identifiers attached to each
+ * tool's `_meta['io.mcpmed/concepts']` field. Each constant is a stable URI
+ * from an established vocabulary (Schema.org or EDAM) paired with a human
+ * label — no free-text placeholders.
+ *
+ * This implements the semantic concept mapping proposed in MCPmed
+ * (Flotho et al., Briefings in Bioinformatics, 2026; doi:10.1093/bib/bbag076)
+ * with resolvable URIs rather than the placeholder strings used in that paper's
+ * reference implementations.
+ *
+ * Namespacing: the `io.mcpmed/concepts` key is a proposal for MCPmed-aligned
+ * servers. If MCPmed standardizes a different key, this is a single rename.
+ *
+ * @module src/mcp-server/tools/definitions/_concepts
+ */
+/** A single ontology-backed concept tag. */
+export interface ConceptTag {
+    readonly id: string;
+    readonly label: string;
+}
+export declare const SCHEMA_SEARCH_ACTION: ConceptTag;
+export declare const SCHEMA_SCHOLARLY_ARTICLE: ConceptTag;
+export declare const SCHEMA_CREATIVE_WORK: ConceptTag;
+export declare const SCHEMA_DEFINED_TERM: ConceptTag;
+export declare const SCHEMA_DEFINED_TERM_SET: ConceptTag;
+export declare const EDAM_DATABASE_SEARCH: ConceptTag;
+export declare const EDAM_DATA_RETRIEVAL: ConceptTag;
+export declare const EDAM_ID_MAPPING: ConceptTag;
+export declare const EDAM_DATA_FORMATTING: ConceptTag;
+export declare const EDAM_ONTOLOGY_TERMINOLOGY: ConceptTag;
+export declare const EDAM_PUBMED_ID: ConceptTag;
+export declare const EDAM_ACCESSION: ConceptTag;
+/**
+ * Builds the `_meta` payload emitted alongside each tool definition.
+ * Kept as a helper so the key namespace is declared exactly once.
+ */
+export declare function conceptMeta(concepts: readonly ConceptTag[]): {
+    'io.mcpmed/concepts': readonly ConceptTag[];
+};
+//# sourceMappingURL=_concepts.d.ts.map

package/dist/mcp-server/tools/definitions/_concepts.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/mcp-server/tools/definitions/_concepts.js ADDED Viewed

@@ -0,0 +1,74 @@
+/**
+ * @fileoverview Ontology-backed semantic concept identifiers attached to each
+ * tool's `_meta['io.mcpmed/concepts']` field. Each constant is a stable URI
+ * from an established vocabulary (Schema.org or EDAM) paired with a human
+ * label — no free-text placeholders.
+ *
+ * This implements the semantic concept mapping proposed in MCPmed
+ * (Flotho et al., Briefings in Bioinformatics, 2026; doi:10.1093/bib/bbag076)
+ * with resolvable URIs rather than the placeholder strings used in that paper's
+ * reference implementations.
+ *
+ * Namespacing: the `io.mcpmed/concepts` key is a proposal for MCPmed-aligned
+ * servers. If MCPmed standardizes a different key, this is a single rename.
+ *
+ * @module src/mcp-server/tools/definitions/_concepts
+ */
+// Schema.org — generic web entities and actions.
+export const SCHEMA_SEARCH_ACTION = {
+    id: 'https://schema.org/SearchAction',
+    label: 'Search action',
+};
+export const SCHEMA_SCHOLARLY_ARTICLE = {
+    id: 'https://schema.org/ScholarlyArticle',
+    label: 'Scholarly article',
+};
+export const SCHEMA_CREATIVE_WORK = {
+    id: 'https://schema.org/CreativeWork',
+    label: 'Creative work',
+};
+export const SCHEMA_DEFINED_TERM = {
+    id: 'https://schema.org/DefinedTerm',
+    label: 'Defined term',
+};
+export const SCHEMA_DEFINED_TERM_SET = {
+    id: 'https://schema.org/DefinedTermSet',
+    label: 'Defined term set',
+};
+// EDAM ontology — bioinformatics operations, data, and topics.
+export const EDAM_DATABASE_SEARCH = {
+    id: 'https://edamontology.org/operation_2421',
+    label: 'Database search',
+};
+export const EDAM_DATA_RETRIEVAL = {
+    id: 'https://edamontology.org/operation_2422',
+    label: 'Data retrieval',
+};
+export const EDAM_ID_MAPPING = {
+    id: 'https://edamontology.org/operation_3282',
+    label: 'ID mapping',
+};
+export const EDAM_DATA_FORMATTING = {
+    id: 'https://edamontology.org/operation_0335',
+    label: 'Data formatting',
+};
+export const EDAM_ONTOLOGY_TERMINOLOGY = {
+    id: 'https://edamontology.org/topic_0089',
+    label: 'Ontology and terminology',
+};
+export const EDAM_PUBMED_ID = {
+    id: 'https://edamontology.org/data_1187',
+    label: 'PubMed ID',
+};
+export const EDAM_ACCESSION = {
+    id: 'https://edamontology.org/data_2091',
+    label: 'Accession',
+};
+/**
+ * Builds the `_meta` payload emitted alongside each tool definition.
+ * Kept as a helper so the key namespace is declared exactly once.
+ */
+export function conceptMeta(concepts) {
+    return { 'io.mcpmed/concepts': concepts };
+}
+//# sourceMappingURL=_concepts.js.map

package/dist/mcp-server/tools/definitions/_concepts.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBA+EzB,CAAC"}

package/dist/mcp-server/tools/definitions/convert-ids.tool.js CHANGED Viewed

@@ -5,9 +5,12 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
+import { conceptMeta, EDAM_ACCESSION, EDAM_ID_MAPPING } from './_concepts.js';
 export const convertIdsTool = tool('pubmed_convert_ids', {
     description: `Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Uses the NCBI PMC ID Converter API — only resolves articles indexed in PubMed Central. For articles not in PMC, use pubmed_search_articles instead.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([EDAM_ID_MAPPING, EDAM_ACCESSION]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/convert-ids.tool.ts',
     input: z.object({
         ids: z
             .array(z.string().min(1))

package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAajD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA4P5B,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED Viewed

@@ -7,10 +7,13 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 export const fetchArticlesTool = tool('pubmed_fetch_articles', {
     description: 'Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms.',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-articles.tool.ts',
     input: z.object({
         pmids: z.array(pmidStringSchema).min(1).max(200).describe('PubMed IDs to fetch'),
         includeMesh: z.boolean().default(true).describe('Include MeSH terms'),

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAiDjD~~,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~kBAmO5B~~,CAAC"}
1	+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAsO5B,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED Viewed

@@ -7,6 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { parsePmcArticle } from '../../../services/ncbi/parsing/pmc-article-parser.js';
 import { findAll, findOne } from '../../../services/ncbi/parsing/pmc-xml-helpers.js';
+import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 function normalizePmcId(id) {
     return id.replace(/^PMC/i, '');
@@ -40,6 +41,8 @@ const SectionSchema = z.object({
 export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
     description: 'Fetch full-text articles from PubMed Central (PMC). Returns complete article body text, sections, and references for open-access articles. Accepts PMC IDs directly or PubMed IDs (auto-resolved via the PMC ID Converter).',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-fulltext.tool.ts',
     input: z.object({
         pmcids: z
             .array(z.string())

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAmCjD~~,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;~~kBA8J1B~~,CAAC"}
1	+ {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;kBAiK1B,CAAC"}

package/dist/mcp-server/tools/definitions/find-related.tool.js CHANGED Viewed

@@ -7,6 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 function extractValue(field) {
     if (field === undefined || field === null)
@@ -19,6 +20,8 @@ function extractValue(field) {
 export const findRelatedTool = tool('pubmed_find_related', {
     description: 'Find articles related to a source article — similar content, citing articles, or references.',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/find-related.tool.ts',
     input: z.object({
         pmid: pmidStringSchema.describe('Source PubMed ID'),
         relationship: z

package/dist/mcp-server/tools/definitions/find-related.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAWjD~~,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;~~kBAuF9B~~,CAAC"}
1	+ {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAYjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;kBA0F9B,CAAC"}

package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED Viewed

@@ -8,10 +8,13 @@ import { formatCitations, } from '../../../services/ncbi/formatting/citation-for
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { conceptMeta, EDAM_DATA_FORMATTING, SCHEMA_CREATIVE_WORK } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 export const formatCitationsTool = tool('pubmed_format_citations', {
     description: 'Get formatted citations for PubMed articles in APA, MLA, BibTeX, or RIS format.',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([SCHEMA_CREATIVE_WORK, EDAM_DATA_FORMATTING]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/format-citations.tool.ts',
     input: z.object({
         pmids: z.array(pmidStringSchema).min(1).max(50).describe('PubMed IDs to cite'),
         styles: z

package/dist/mcp-server/tools/definitions/format-citations.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACzF,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,CAAC,CAAC;IAChE,SAAS,EACP,oHAAoH;IAEtH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;aAC9C,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC;aAChB,QAAQ,CAAC,6BAA6B,CAAC;KAC3C,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC,CACH;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,CACtD,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,IAAI,KAAK,CAAC,gCAAgC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC5E,CAAC;QAED,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,MAAyB,CAAC;aACpE,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAIjD~~,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;~~kBAwH7B~~,CAAC"}
1	+ {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;kBA2H7B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js CHANGED Viewed

@@ -5,9 +5,12 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
+import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
 export const lookupCitationTool = tool('pubmed_lookup_citation', {
     description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID. Uses NCBI ECitMatch for deterministic matching — more reliable than searching by citation fields.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
     input: z.object({
         citations: z
             .array(z.object({

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoFjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;kBAwFzB,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js CHANGED Viewed

@@ -6,6 +6,7 @@
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { ensureArray, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_ONTOLOGY_TERMINOLOGY, SCHEMA_DEFINED_TERM, SCHEMA_DEFINED_TERM_SET, } from './_concepts.js';
 function findItem(items, name) {
     return items.find((it) => getText(it['@_Name']) === name);
 }
@@ -70,6 +71,13 @@ function parseSummaryRecords(data, ids, includeDetails) {
 export const lookupMeshTool = tool('pubmed_lookup_mesh', {
     description: 'Search and explore MeSH (Medical Subject Headings) vocabulary. Essential for building precise PubMed queries.',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([
+        SCHEMA_DEFINED_TERM,
+        SCHEMA_DEFINED_TERM_SET,
+        EDAM_ONTOLOGY_TERMINOLOGY,
+        EDAM_DATA_RETRIEVAL,
+    ]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-mesh.tool.ts',
     input: z.object({
         term: z.string().min(1).describe('MeSH term to look up'),
         maxResults: z.number().int().min(1).max(50).default(10).describe('Maximum results'),

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA2S7B,CAAC"}

package/dist/mcp-server/tools/definitions/search-articles.tool.js CHANGED Viewed

@@ -7,6 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { sanitization } from '@cyanheads/mcp-ts-core/utils';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
+import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
 /**
  * Accepts empty strings (treated as "no filter" by the handler) or dates in
  * YYYY, YYYY/MM, or YYYY/MM/DD form with `/`, `-`, or `.` separators.
@@ -67,6 +68,8 @@ const AppliedFiltersSchema = z.object({
 export const searchArticlesTool = tool('pubmed_search_articles', {
     description: '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.',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/search-articles.tool.ts',
     input: z.object({
         query: z.string().min(1).describe('PubMed search query (supports full NCBI syntax)'),
         maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),

package/dist/mcp-server/tools/definitions/search-articles.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAGjD~~,eAAO,MAAM,cAAc;;;;;;~~kBAyCzB~~,CAAC"}
1	+ {"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,cAAc;;;;;;kBA4CzB,CAAC"}

package/dist/mcp-server/tools/definitions/spell-check.tool.js CHANGED Viewed

@@ -5,9 +5,12 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
+import { conceptMeta, SCHEMA_SEARCH_ACTION } from './_concepts.js';
 export const spellCheckTool = tool('pubmed_spell_check', {
     description: "Spell-check a query and get NCBI's suggested correction. Useful for refining search queries.",
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([SCHEMA_SEARCH_ACTION]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/spell-check.tool.ts',
     input: z.object({
         query: z.string().min(2).describe('PubMed search query to spell-check'),
     }),

package/dist/mcp-server/tools/definitions/spell-check.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.4.1",
+  "version": "2.5.0",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
   "type": "module",
@@ -67,7 +67,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.5.3",
+    "@cyanheads/mcp-ts-core": "^0.6.3",
     "fast-xml-parser": "^5.7.1",
     "pino-pretty": "^13.1.3",
     "sanitize-html": "^2.17.3"
@@ -76,11 +76,11 @@
     "@biomejs/biome": "^2.4.12",
     "@types/node": "^25.6.0",
     "@types/sanitize-html": "^2.16.1",
-    "@vitest/coverage-istanbul": "^4.1.4",
+    "@vitest/coverage-istanbul": "^4.1.5",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.16",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.4"
+    "vitest": "^4.1.5"
   }
 }

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.4.1",
+  "version": "2.5.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.4.1",
+      "version": "2.5.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -60,7 +60,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.4.1",
+      "version": "2.5.0",
       "packageArguments": [
         {
           "type": "positional",