@digital-science-dsl/dimensions-analytics-mcp 1.1.0 → 1.3.0

package/src/mcp/examples/dsl-examples.ts

@@ -12,11 +12,13 @@ export const DSL_EXAMPLES_BY_ENTITY: Record<string, readonly string[]> = {
     'search publications for "machine learning" return publications[id+title+doi] limit 10',
     'search publications for "CRISPR" where year >= 2020 return publications[id+title+times_cited+year] sort by times_cited desc limit 25',
     'search publications in title_only for "gene therapy" return publications[basics] limit 10',
+    'search publications for similar_documents("After spinal cord injury, macrophages infiltrate the lesion site") where year > 2015 return publications[id+title+year] sort by score desc limit 5',
     "search publications return publications facet journal limit 20",
   ],
   grants: [
     'search grants for "cancer immunotherapy" return grants limit 10',
     'search grants where funder_org_name = "National Institutes of Health" return grants[basics] limit 10',
+    'search grants for similar_documents("Cancer immunotherapy with checkpoint inhibitors and CAR-T") where start_year >= 2020 return grants[id+title] sort by score desc limit 5',
     "search grants return grants aggregate funding_usd",
   ],
   patents: [
@@ -53,13 +55,15 @@ export const DSL_EXAMPLES_BY_ENTITY: Record<string, readonly string[]> = {
   ],
 };
 
-/** General DSL patterns (describe, functions, pagination). */
+/** General DSL patterns (describe, functions, pagination, similarity). */
 export const DSL_GENERAL_EXAMPLES = [
   "describe version",
   "describe schema",
   "describe source publications",
   'extract_concepts(text: "CRISPR gene editing enables precise DNA modification")',
   'classify(text: "Stem cell therapy for diabetes", system: "for")',
+  'search publications for similar_documents("After spinal cord injury, macrophages infiltrate the lesion site") where year > 2015 return publications[id+title+year] sort by score desc limit 5',
+  'search grants for similar_documents("Cancer immunotherapy with checkpoint inhibitors and CAR-T") where start_year >= 2020 return grants[id+title] sort by score desc limit 5',
 ] as const;
 
 /** Link to official DSL documentation. */

package/src/mcp/examples/usage-scenarios.ts

@@ -164,6 +164,44 @@ export const USAGE_SCENARIOS: readonly UsageScenario[] = [
     },
     dslContains: ["large language model", "citations_per_year(2018, 2024)"],
   },
+  {
+    id: "similar-documents",
+    goal: "Similar papers from an abstract",
+    prompt: "Find publications similar to this abstract about spinal cord injury macrophages.",
+    tool: "similar_documents",
+    args: {
+      entityType: "publications",
+      text: "After spinal cord injury, macrophages infiltrate the lesion site and contribute to both tissue damage and repair processes.",
+      yearFrom: 2016,
+      limit: 10,
+      fields: ["id", "title", "year"],
+    },
+    dslContains: [
+      "search publications for similar_documents(",
+      "year >= 2016",
+      "sort by score desc",
+      "limit 10",
+    ],
+  },
+  {
+    id: "similar-grants",
+    goal: "Similar grants from a description",
+    prompt: "Find grants similar to this description of CAR-T cancer immunotherapy.",
+    tool: "similar_documents",
+    args: {
+      entityType: "grants",
+      text: "Development of novel cancer immunotherapy approaches using checkpoint inhibitors and CAR-T cell engineering for solid tumors.",
+      yearFrom: 2020,
+      limit: 10,
+      fields: ["id", "title", "funding_usd", "start_year"],
+    },
+    dslContains: [
+      "search grants for similar_documents(",
+      "start_year >= 2020",
+      "sort by score desc",
+      "limit 10",
+    ],
+  },
   {
     id: "build-complex-query",
     goal: "Build a complex query",

package/src/mcp/http-server.ts

@@ -5,8 +5,8 @@
 
 import { randomUUID } from "node:crypto";
 import type { IncomingMessage, Server } from "node:http";
-import { createMcpExpressApp } from "@modelcontextprotocol/sdk/server/express.js";
-import { StreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/streamableHttp.js";
+import { createMcpExpressApp } from "@modelcontextprotocol/express";
+import { NodeStreamableHTTPServerTransport } from "@modelcontextprotocol/node";
 import type { Request, Response } from "express";
 import type { HostedEnvConfig } from "../client/deployment-config.js";
 import { AuthenticationError } from "../client/errors.js";
@@ -73,7 +73,7 @@ export function startHostedHttpServer(options: HostedHttpServerOptions): HostedH
         mcpClient,
       });
 
-      const transport = new StreamableHTTPServerTransport({
+      const transport = new NodeStreamableHTTPServerTransport({
         sessionIdGenerator: undefined,
       });
 

package/src/mcp/middleware/field-aliases.ts

@@ -4,8 +4,7 @@
  * via a higher-order function (decorator) pattern.
  * @module mcp/middleware/field-aliases
  */
-
-import type { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
+import type { CallToolResult } from "@modelcontextprotocol/server";
 import type { EntityType } from "../../dsl/index.js";
 
 // ---------------------------------------------------------------------------

package/src/mcp/resources/schema.ts

@@ -3,8 +3,8 @@
  * @module mcp/resources/schema
  */
 
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { ResourceTemplate } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { McpServer } from "@modelcontextprotocol/server";
+import { ResourceTemplate } from "@modelcontextprotocol/server";
 import {
   buildUsagePolicy,
   type DescribeField,
@@ -32,7 +32,7 @@ import type { SchemaContext } from "../schema/context.js";
  */
 export function registerSchemaResources(server: McpServer, context: SchemaContext): void {
   const schemaStore = () => context.store;
-  server.resource(
+  server.registerResource(
     "schema-summary",
     "dimensions://schema/summary",
     {
@@ -52,7 +52,7 @@ export function registerSchemaResources(server: McpServer, context: SchemaContex
   );
 
   // Full schema
-  server.resource(
+  server.registerResource(
     "schema-full",
     "dimensions://schema",
     {
@@ -72,7 +72,7 @@ export function registerSchemaResources(server: McpServer, context: SchemaContex
   );
 
   // Version
-  server.resource(
+  server.registerResource(
     "schema-version",
     "dimensions://schema/version",
     {
@@ -95,7 +95,7 @@ export function registerSchemaResources(server: McpServer, context: SchemaContex
   );
 
   // Limits (static until upstream `describe limits` exists)
-  server.resource(
+  server.registerResource(
     "schema-limits",
     "dimensions://schema/limits",
     {
@@ -113,7 +113,7 @@ export function registerSchemaResources(server: McpServer, context: SchemaContex
     }),
   );
 
-  server.resource(
+  server.registerResource(
     "schema-policy",
     "dimensions://schema/policy",
     {
@@ -132,7 +132,7 @@ export function registerSchemaResources(server: McpServer, context: SchemaContex
     }),
   );
 
-  server.resource(
+  server.registerResource(
     "dsl-examples",
     "dimensions://examples",
     {
@@ -160,7 +160,7 @@ export function registerSchemaResources(server: McpServer, context: SchemaContex
     }),
   );
 
-  server.resource(
+  server.registerResource(
     "dsl-examples-by-source",
     new ResourceTemplate("dimensions://examples/{source}", {
       list: async () => ({
@@ -219,7 +219,7 @@ export function registerSchemaResources(server: McpServer, context: SchemaContex
   );
 
   const sourceNames = () => schemaStore().sourceNames();
-  server.resource(
+  server.registerResource(
     "schema-sources",
     new ResourceTemplate("dimensions://schema/sources/{sourceName}", {
       list: async () => ({
@@ -256,7 +256,7 @@ export function registerSchemaResources(server: McpServer, context: SchemaContex
   );
 
   const entityNames = () => schemaStore().entityNames();
-  server.resource(
+  server.registerResource(
     "schema-entities",
     new ResourceTemplate("dimensions://schema/entities/{entityName}", {
       list: async () => ({
@@ -294,7 +294,7 @@ export function registerSchemaResources(server: McpServer, context: SchemaContex
 
   // Compatibility view for structured search tools
   const entityTypes = () => schemaStore().structuredEntityTypes();
-  server.resource(
+  server.registerResource(
     "fields",
     new ResourceTemplate("dimensions://fields/{entityType}", {
       list: async () => ({

package/src/mcp/server.ts

@@ -4,9 +4,9 @@
  * @module mcp/server
  */
 
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
-import type { Transport } from "@modelcontextprotocol/sdk/shared/transport.js";
+import type { Transport } from "@modelcontextprotocol/server";
+import { McpServer } from "@modelcontextprotocol/server";
+import { StdioServerTransport } from "@modelcontextprotocol/server/stdio";
 import pkg from "../../package.json" with { type: "json" };
 import { type HostedEnvConfig, loadDeploymentConfig } from "../client/index.js";
 import { createBootstrapDimensionsClient, createDimensionsClient } from "../dsl/create-client.js";
@@ -27,6 +27,7 @@ import { registerLookupTools } from "./tools/lookup.js";
 import { registerQueryTools } from "./tools/query.js";
 import { registerSchemaTools, validateFieldAliases } from "./tools/schema.js";
 import { registerSearchTools } from "./tools/search.js";
+import { registerSimilarDocumentsTool } from "./tools/similar-documents.js";
 import { initMcpUsageTracking } from "./usage-tracking.js";
 
 /**
@@ -94,7 +95,7 @@ export function buildServerInstructions(schemaStore: SchemaStore): string {
     [
       "Workflow:",
       "(1) Discover schema — read dimensions://schema/summary, dimensions://fields/{entity}, dimensions://examples/{source}, or describe_schema;",
-      "(2) Search — search_* for keyword discovery with filters; get_by_doi, get_by_pmid, get_by_id for known identifiers;",
+      "(2) Search — search_* for keyword discovery with filters; similar_documents for topic-similar pubs/grants from abstract text; get_by_doi, get_by_pmid, get_by_id for known identifiers;",
       "(3) Analyze — facet_query, aggregate_query, citation_trend, funding_trend;",
       "(4) Drill down — get_by_id, search_* with filters (e.g. researchers.id, research_orgs.id), facet_query for top researchers at an org.",
     ].join(" "),
@@ -105,12 +106,14 @@ export function buildServerInstructions(schemaStore: SchemaStore): string {
       "search_organizations for institution lookup — prefer GRID id in filters when the name is ambiguous;",
       "search_source_titles for journals / ISSN lookup (not articles); search_reports for technical reports;",
       "search_funder_groups / search_research_org_groups for curated group name → member GRID ids;",
+      "similar_documents finds concept-similar publications/grants from prose (not embeddings); for a known ID, get_by_id then pass abstract/description as text;",
       "facet_query supports yearFrom/yearTo for year-scoped facets.",
     ].join(" "),
     [
       "Query construction:",
       "for ranked publication search (e.g. most-cited since 2020), use search_publications with query, yearFrom, sortBy (times_cited or total_citations), limit — do not hand-write execute_dsl;",
-      "use execute_dsl for boolean concept groups and DSL special functions;",
+      "for similar-document lookup, use similar_documents — do not hand-write similar_documents() in execute_dsl;",
+      "use execute_dsl for boolean concept groups and remaining DSL special functions (classify, extract_concepts);",
       "use execute_dsl only when structured tools are insufficient; DSL order is return ... sort by FIELD order limit N (never limit before sort).",
     ].join(" "),
     [
@@ -138,6 +141,7 @@ function registerAllTools(
   registerLookupTools(server, client);
   registerQueryTools(server, client, schemaStore);
   registerFunctionTools(server, client);
+  registerSimilarDocumentsTool(server, client);
   registerAnalyticsTools(server, client, schemaStore);
   registerSchemaTools(server, client, schemaContext);
 }

package/src/mcp/tools/analytics.ts

@@ -4,8 +4,8 @@
  * @module mcp/tools/analytics
  */
 
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { ErrorCode, McpError } from "@modelcontextprotocol/sdk/types.js";
+import type { McpServer } from "@modelcontextprotocol/server";
+import { ProtocolError, ProtocolErrorCode } from "@modelcontextprotocol/server";
 import { z } from "zod";
 import type { Currency, DimensionsClient, EntityType } from "../../dsl/index.js";
 import {
@@ -60,8 +60,8 @@ function entityTypeEnum(schemaStore: SchemaStore) {
 function assertFacetField(schemaStore: SchemaStore, entity: string, facetField: string): void {
   const valid = schemaStore.facetFields(entity);
   if (!valid.includes(facetField)) {
-    throw new McpError(
-      ErrorCode.InvalidParams,
+    throw new ProtocolError(
+      ProtocolErrorCode.InvalidParams,
       `Invalid facet field "${facetField}" for entity "${entity}". Valid fields: ${valid.join(", ") || "(none)"}`,
     );
   }
@@ -77,8 +77,8 @@ function assertIndicators(schemaStore: SchemaStore, entity: string, indicators:
   const valid = new Set(schemaStore.metrics(entity));
   const invalid = indicators.filter((name) => !valid.has(name));
   if (invalid.length > 0) {
-    throw new McpError(
-      ErrorCode.InvalidParams,
+    throw new ProtocolError(
+      ProtocolErrorCode.InvalidParams,
       `Invalid indicator(s) for entity "${entity}": ${invalid.join(", ")}. Valid metrics: ${[...valid].join(", ") || "(none)"}`,
     );
   }
@@ -131,7 +131,7 @@ export function registerAnalyticsTools(
       description:
         "Distribution analysis across entity dimensions. Returns facet buckets showing how records " +
         "are distributed across a categorical field. Example: 'What journals publish the most CRISPR research?'",
-      inputSchema: {
+      inputSchema: z.object({
         entityType: entityTypeSchema,
         facetField: z
           .string()
@@ -165,13 +165,13 @@ export function registerAnalyticsTools(
           .array(ExtendedWhereFilterSchema)
           .optional()
           .describe("Additional where-clause filters before faceting"),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         entityType: z.string().describe("Entity type analyzed"),
         facetField: z.string().describe("Field faceted on"),
         totalBuckets: z.number().describe("Number of facet buckets returned"),
         buckets: z.array(z.record(z.string(), z.unknown())).describe("Facet bucket distribution"),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     withFieldAliases(
@@ -221,7 +221,7 @@ export function registerAnalyticsTools(
       description:
         "Metric aggregation on facet buckets. Returns facet buckets enriched with aggregated indicator " +
         "values. Example: 'Which funders have the highest average citation ratio?'",
-      inputSchema: {
+      inputSchema: z.object({
         entityType: entityTypeSchema,
         facetField: z
           .string()
@@ -263,8 +263,8 @@ export function registerAnalyticsTools(
           .array(ExtendedWhereFilterSchema)
           .optional()
           .describe("Additional where-clause filters before aggregating"),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         entityType: z.string().describe("Entity type analyzed"),
         facetField: z.string().describe("Field faceted on"),
         indicators: z.array(z.string()).describe("Aggregation indicators computed"),
@@ -272,7 +272,7 @@ export function registerAnalyticsTools(
         buckets: z
           .array(z.record(z.string(), z.unknown()))
           .describe("Facet buckets with aggregated values"),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     withFieldAliases(
@@ -330,7 +330,7 @@ export function registerAnalyticsTools(
       description:
         "Year-by-year citation counts for a topic. Returns annual citation totals for publications " +
         "matching the query over the specified year range.",
-      inputSchema: {
+      inputSchema: z.object({
         query: z
           .string()
           .min(1)
@@ -347,22 +347,22 @@ export function registerAnalyticsTools(
           .min(1900)
           .max(2100)
           .describe("Last year of the time range (inclusive)"),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         query: z.string().describe("Search query used"),
         startYear: z.number().describe("First year of range"),
         endYear: z.number().describe("Last year of range"),
         citationsPerYear: z
           .array(z.record(z.string(), z.unknown()))
           .describe("Annual citation totals"),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     async (args) => {
       try {
         if (args.startYear > args.endYear) {
-          throw new McpError(
-            ErrorCode.InvalidParams,
+          throw new ProtocolError(
+            ProtocolErrorCode.InvalidParams,
             `startYear (${args.startYear}) must be ≤ endYear (${args.endYear})`,
           );
         }
@@ -393,7 +393,7 @@ export function registerAnalyticsTools(
       description:
         "Year-by-year funding totals for a topic. Returns annual grant funding amounts for grants " +
         "matching the query over the specified year range.",
-      inputSchema: {
+      inputSchema: z.object({
         query: z
           .string()
           .min(1)
@@ -416,8 +416,8 @@ export function registerAnalyticsTools(
           .describe(
             `Currency for funding amounts (default USD). Supported: ${SUPPORTED_CURRENCIES.join(", ")}.`,
           ),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         query: z.string().describe("Search query used"),
         startYear: z.number().describe("First year of range"),
         endYear: z.number().describe("Last year of range"),
@@ -425,14 +425,14 @@ export function registerAnalyticsTools(
         fundingPerYear: z
           .array(z.record(z.string(), z.unknown()))
           .describe("Annual funding totals"),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     async (args) => {
       try {
         if (args.startYear > args.endYear) {
-          throw new McpError(
-            ErrorCode.InvalidParams,
+          throw new ProtocolError(
+            ProtocolErrorCode.InvalidParams,
             `startYear (${args.startYear}) must be ≤ endYear (${args.endYear})`,
           );
         }

package/src/mcp/tools/fetch-search-pages.ts

@@ -3,8 +3,7 @@
  * Supports single-page, aggregate, and JSONL file export modes.
  * @module mcp/tools/fetch-search-pages
  */
-
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { McpServer } from "@modelcontextprotocol/server";
 import { z } from "zod";
 import { ValidationError } from "../../client/index.js";
 import {
@@ -95,7 +94,7 @@ export function registerFetchSearchPagesTools(
         "Default mode returns one page. Use aggregate for ID counts/sums without full rows. " +
         "Use file mode to stream JSONL or CSV locally — never for bulk mirroring of Dimensions data. " +
         `Entities: ${entityList}.`,
-      inputSchema: {
+      inputSchema: z.object({
         entityType: z
           .enum(STRUCTURED_ENTITY_TYPES)
           .describe("Dimensions source to search (same as search_* tools)"),
@@ -156,8 +155,8 @@ export function registerFetchSearchPagesTools(
           .describe(
             "Required when maxPages > 5 or planned records > 5000. Acknowledges reasonable-use policy.",
           ),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         mode: z.string(),
         entityType: z.string(),
         totalCount: z.number().optional(),
@@ -176,7 +175,7 @@ export function registerFetchSearchPagesTools(
             totalFundingUsd: z.number().optional(),
           })
           .optional(),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     withFieldAliases(

package/src/mcp/tools/functions.ts

@@ -3,8 +3,7 @@
  * Entity resolution helpers (affiliations, grants).
  * @module mcp/tools/functions
  */
-
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { McpServer } from "@modelcontextprotocol/server";
 import { z } from "zod";
 import type { DimensionsClient } from "../../dsl/index.js";
 import { registerTrackedTool } from "../usage-tracking.js";
@@ -24,7 +23,7 @@ export function registerFunctionTools(server: McpServer, client: DimensionsClien
         "Resolve and disambiguate organization affiliations using Dimensions entity resolution. " +
         "Takes freetext affiliation strings or structured organization data and returns matched " +
         "organizations with GRID/ROR identifiers and confidence scores.",
-      inputSchema: {
+      inputSchema: z.object({
         affiliations: z
           .array(
             z.object({
@@ -42,11 +41,11 @@ export function registerFunctionTools(server: McpServer, client: DimensionsClien
           .describe(
             "Array of affiliations to resolve. Each must have either 'affiliation' or 'name'",
           ),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         matchCount: z.number().describe("Number of resolved affiliations"),
         affiliations: z.array(z.record(z.string(), z.unknown())).describe("Resolved affiliations"),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     async (args) => {
@@ -71,7 +70,7 @@ export function registerFunctionTools(server: McpServer, client: DimensionsClien
         "Resolve grant numbers to Dimensions grant records. " +
         "Takes a grant number and optional funder information to find matching grants " +
         "with full metadata including funding amounts, dates, and funder details.",
-      inputSchema: {
+      inputSchema: z.object({
         grant_number: z.string().min(1).describe("Grant number to look up (e.g., 'R01HL117329')"),
         fundref: z
           .string()
@@ -81,11 +80,11 @@ export function registerFunctionTools(server: McpServer, client: DimensionsClien
           .string()
           .optional()
           .describe("Funder name as alternative to FundRef ID (e.g., 'NIH')"),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         matchCount: z.number().describe("Number of matched grants"),
         grants: z.array(z.record(z.string(), z.unknown())).describe("Matched grant records"),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     async (args) => {

package/src/mcp/tools/lookup.ts

@@ -3,8 +3,7 @@
  * Provides direct lookup by identifiers (DOI, PMID, Dimensions ID).
  * @module mcp/tools/lookup
  */
-
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { McpServer } from "@modelcontextprotocol/server";
 import { z } from "zod";
 import { type DimensionsClient, EntitySchema, type EntityType } from "../../dsl/index.js";
 import { withFieldAliases } from "../middleware/field-aliases.js";
@@ -29,18 +28,18 @@ export function registerLookupTools(server: McpServer, client: DimensionsClient)
     {
       description:
         "Retrieve a publication by its Digital Object Identifier (DOI). Returns full publication details including abstract, citations, and authors.",
-      inputSchema: {
+      inputSchema: z.object({
         doi: z.string().describe("The DOI to look up (e.g., '10.1038/nature12373')"),
         fields: z
           .array(z.string())
           .optional()
           .describe("Fields to return (e.g., ['id', 'title', 'abstract', 'times_cited'])"),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         found: z.boolean().describe("Whether the entity was found"),
         publication: z.record(z.string(), z.unknown()).optional().describe("The found entity"),
         message: z.string().optional().describe("Message when not found"),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     withFieldAliases(
@@ -83,18 +82,18 @@ export function registerLookupTools(server: McpServer, client: DimensionsClient)
     {
       description:
         "Retrieve a publication by its PubMed ID (PMID). Returns full publication details from Dimensions.",
-      inputSchema: {
+      inputSchema: z.object({
         pmid: z.string().describe("The PubMed ID to look up (e.g., '23846567')"),
         fields: z
           .array(z.string())
           .optional()
           .describe("Fields to return (e.g., ['id', 'title', 'abstract', 'times_cited'])"),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         found: z.boolean().describe("Whether the entity was found"),
         publication: z.record(z.string(), z.unknown()).optional().describe("The found entity"),
         message: z.string().optional().describe("Message when not found"),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     withFieldAliases(
@@ -137,17 +136,17 @@ export function registerLookupTools(server: McpServer, client: DimensionsClient)
     {
       description:
         "Retrieve any entity by its Dimensions ID. Supports publications, grants, patents, clinical trials, datasets, policy documents, researchers, organizations, reports, source titles, funder groups, and research org groups.",
-      inputSchema: {
+      inputSchema: z.object({
         entityType: EntitySchema.describe("The type of entity to look up"),
         id: z.string().describe("The Dimensions ID to look up"),
         fields: z.array(z.string()).optional().describe("Fields to return"),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         found: z.boolean().describe("Whether the entity was found"),
         entity: z.record(z.string(), z.unknown()).optional().describe("The found entity"),
         entityType: z.string().optional().describe("The type of the found entity"),
         message: z.string().optional().describe("Message when not found"),
-      },
+      }),
       annotations: READ_ONLY_API_ANNOTATIONS,
     },
     withFieldAliases(

package/src/mcp/tools/query.ts

@@ -3,8 +3,7 @@
  * Provides raw DSL query execution for power users.
  * @module mcp/tools/query
  */
-
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { McpServer } from "@modelcontextprotocol/server";
 import { z } from "zod";
 import {
   buildExecuteDslPolicyHints,
@@ -47,7 +46,7 @@ Examples:
 - return funders aggregate funding_usd
 
 Structured entity types: ${sources}`,
-      inputSchema: {
+      inputSchema: z.object({
         dsl: z.string().describe("Complete DSL query string to execute"),
         confirmLargeFetch: z
           .boolean()
@@ -56,8 +55,8 @@ Structured entity types: ${sources}`,
           .describe(
             "Required for deep pagination in DSL (skip≥5000). See dimensions://schema/policy.",
           ),
-      },
-      outputSchema: {
+      }),
+      outputSchema: z.object({
         result: z.record(z.string(), z.unknown()).describe("Raw DSL query response"),
         policyNotice: z.string().optional().describe("Reasonable-use reminder"),
         largeResultWarning: z
@@ -68,7 +67,7 @@ Structured entity types: ${sources}`,
           .string()
           .optional()
           .describe("Pagination guidance when results are truncated"),
-      },
+      }),
       annotations: {
         readOnlyHint: true,
         destructiveHint: false,