@digital-science-dsl/dimensions-analytics-mcp 0.5.3

package/dist/tools/dataset-profile.js

@@ -0,0 +1,194 @@
+/**
+ * Dataset profile tool for the MCP server.
+ * Provides deep profiling of Dimensions datasets including structural links
+ * to associated publications and grants.
+ * @module mcp/tools/dataset-profile
+ */
+import { ErrorCode, McpError } from "@modelcontextprotocol/sdk/types.js";
+import { z } from "zod";
+import { asArray, formatErrorResult, formatToolResult, READ_ONLY_API_ANNOTATIONS, } from "../utils.js";
+/**
+ * Registers the dataset_profile tool with the MCP server.
+ * @param server - MCP server instance
+ * @param client - Dimensions client instance
+ */
+export function registerDatasetProfileTools(server, client) {
+    server.registerTool("dataset_profile", {
+        description: "Get a comprehensive profile for a research dataset including its associated publication, linked grants, and related publications. Uses structural links (associated_publication_id, associated_grant_ids) rather than free-text search.",
+        inputSchema: {
+            datasetId: z.string().optional().describe("Dimensions dataset ID"),
+            query: z
+                .string()
+                .optional()
+                .describe("Search term to find datasets (used when datasetId is not known)"),
+            includeLinkedPublications: z
+                .boolean()
+                .default(true)
+                .describe("Include the associated publication and related publications"),
+            includeLinkedGrants: z.boolean().default(true).describe("Include associated grants"),
+            publicationLimit: z
+                .number()
+                .int()
+                .min(1)
+                .max(50)
+                .default(10)
+                .describe("Max related publications to return"),
+        },
+        outputSchema: {
+            found: z.boolean().describe("Whether the dataset was found"),
+            profile: z
+                .record(z.string(), z.unknown())
+                .optional()
+                .describe("Dataset profile with linked entities"),
+            message: z.string().optional().describe("Message when not found"),
+        },
+        annotations: READ_ONLY_API_ANNOTATIONS,
+    }, async (args) => {
+        if (!args.datasetId && !args.query) {
+            throw new McpError(ErrorCode.InvalidParams, "Must provide at least one of: datasetId or query");
+        }
+        try {
+            // Step 1: Find the dataset
+            let datasetDsl;
+            if (args.datasetId) {
+                datasetDsl = client
+                    .createQueryBuilder()
+                    .search("datasets")
+                    .where("id", "=", args.datasetId)
+                    .fields([
+                    "id",
+                    "title",
+                    "doi",
+                    "year",
+                    "repository",
+                    "description",
+                    "associated_publication_id",
+                    "associated_grant_ids",
+                ])
+                    .limit(1)
+                    .build();
+            }
+            else {
+                datasetDsl = client
+                    .createQueryBuilder()
+                    .search("datasets")
+                    .for(args.query)
+                    .fields([
+                    "id",
+                    "title",
+                    "doi",
+                    "year",
+                    "repository",
+                    "description",
+                    "associated_publication_id",
+                    "associated_grant_ids",
+                ])
+                    .limit(5)
+                    .build();
+            }
+            const datasetResponse = await client.rawQuery(datasetDsl);
+            const datasets = asArray(datasetResponse.datasets);
+            if (datasets.length === 0) {
+                return formatToolResult({
+                    found: false,
+                    message: args.datasetId
+                        ? `No dataset found with ID: ${args.datasetId}`
+                        : `No dataset found matching: ${args.query}`,
+                });
+            }
+            const dataset = datasets[0];
+            const profile = {
+                dataset,
+                matchCount: datasets.length,
+            };
+            // Extract structural link IDs
+            const associatedPubId = typeof dataset.associated_publication_id === "string"
+                ? dataset.associated_publication_id
+                : undefined;
+            const associatedGrantIds = Array.isArray(dataset.associated_grant_ids)
+                ? dataset.associated_grant_ids
+                : undefined;
+            const datasetTitle = typeof dataset.title === "string" ? dataset.title : undefined;
+            // Step 2: Concurrent linked entity fetches
+            const queries = [];
+            if (args.includeLinkedPublications !== false) {
+                // Linked publication via structural ID
+                if (associatedPubId) {
+                    queries.push((async () => {
+                        const pubDsl = client
+                            .createQueryBuilder()
+                            .search("publications")
+                            .where("id", "=", associatedPubId)
+                            .fields([
+                            "id",
+                            "title",
+                            "doi",
+                            "year",
+                            "times_cited",
+                            "journal",
+                            "authors",
+                            "research_orgs",
+                        ])
+                            .limit(1)
+                            .build();
+                        const pubResponse = await client.rawQuery(pubDsl);
+                        const pubs = asArray(pubResponse.publications);
+                        if (pubs.length > 0) {
+                            profile.linkedPublication = pubs[0];
+                        }
+                    })());
+                }
+                // Related publications on same topic
+                if (datasetTitle) {
+                    queries.push((async () => {
+                        const relDsl = client
+                            .createQueryBuilder()
+                            .search("publications")
+                            .for(datasetTitle)
+                            .fields(["id", "title", "doi", "year", "times_cited", "journal"])
+                            .sort("times_cited", "desc")
+                            .limit(args.publicationLimit)
+                            .build();
+                        const relResponse = await client.rawQuery(relDsl);
+                        const relPubs = asArray(relResponse.publications);
+                        profile.relatedPublications = {
+                            totalCount: typeof relResponse._stats?.total_count === "number"
+                                ? relResponse._stats.total_count
+                                : relPubs.length,
+                            returnedCount: relPubs.length,
+                            items: relPubs,
+                        };
+                    })());
+                }
+            }
+            if (args.includeLinkedGrants !== false &&
+                associatedGrantIds &&
+                associatedGrantIds.length > 0) {
+                queries.push((async () => {
+                    const grantDsl = client
+                        .createQueryBuilder()
+                        .search("grants")
+                        .whereIn("id", associatedGrantIds)
+                        .fields(["id", "title", "funding_usd", "funder_org_name", "start_year"])
+                        .limit(10)
+                        .build();
+                    const grantResponse = await client.rawQuery(grantDsl);
+                    const grants = asArray(grantResponse.grants);
+                    profile.linkedGrants = {
+                        totalCount: grants.length,
+                        items: grants,
+                    };
+                })());
+            }
+            await Promise.all(queries);
+            return formatToolResult({
+                found: true,
+                profile,
+            });
+        }
+        catch (error) {
+            return formatErrorResult(error);
+        }
+    });
+}
+//# sourceMappingURL=dataset-profile.js.map

package/dist/tools/dataset-profile.js.map

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package/dist/tools/functions.d.ts

@@ -0,0 +1,14 @@
+/**
+ * Special function tools for the MCP server.
+ * Provides tools for classify, extract_concepts, and similar documents search.
+ * @module mcp/tools/functions
+ */
+import { type DimensionsClient } from "@digital-science/dimensions-dsl";
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+/**
+ * Registers all special function tools with the MCP server.
+ * @param server - MCP server instance
+ * @param client - Dimensions client instance
+ */
+export declare function registerFunctionTools(server: McpServer, client: DimensionsClient): void;
+//# sourceMappingURL=functions.d.ts.map

package/dist/tools/functions.d.ts.map

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package/dist/tools/functions.js

@@ -0,0 +1,294 @@
+/**
+ * Special function tools for the MCP server.
+ * Provides tools for classify, extract_concepts, and similar documents search.
+ * @module mcp/tools/functions
+ */
+import { CLASSIFICATION_SYSTEMS, } from "@digital-science/dimensions-dsl";
+import { ErrorCode, McpError } from "@modelcontextprotocol/sdk/types.js";
+import { z } from "zod";
+import { withFieldAliases } from "../middleware/field-aliases.js";
+import { formatErrorResult, formatToolResult, READ_ONLY_API_ANNOTATIONS } from "../utils.js";
+/**
+ * Registers all special function tools with the MCP server.
+ * @param server - MCP server instance
+ * @param client - Dimensions client instance
+ */
+export function registerFunctionTools(server, client) {
+    // Classify Text
+    server.registerTool("classify_text", {
+        description: "Classify text (title and/or abstract) using Dimensions classification systems. " +
+            "Supports FOR (Fields of Research), SDG (Sustainable Development Goals), RCDC, " +
+            "HRCS, and other research classification taxonomies. Returns classification codes with names.",
+        inputSchema: {
+            title: z
+                .string()
+                .optional()
+                .describe("Document title for classification (at least title or abstract required)"),
+            abstract: z
+                .string()
+                .optional()
+                .describe("Document abstract for classification (at least title or abstract required)"),
+            system: z
+                .enum(CLASSIFICATION_SYSTEMS)
+                .describe("Classification system to use: FOR (Fields of Research), FOR_2020, " +
+                "SDG (Sustainable Development Goals), SDG_2021, RCDC, HRCS_HC, HRCS_RAC, " +
+                "HRA, BRA, ICRP_CSO, ICRP_CT, UOA"),
+        },
+        outputSchema: {
+            system: z.string().describe("Classification system used"),
+            classifications: z
+                .array(z.record(z.string(), z.unknown()))
+                .describe("Classification results"),
+        },
+        annotations: READ_ONLY_API_ANNOTATIONS,
+    }, async (args) => {
+        if (!args.title && !args.abstract) {
+            throw new McpError(ErrorCode.InvalidParams, "At least one of title or abstract must be provided");
+        }
+        try {
+            const result = await client.classify({
+                title: args.title,
+                abstract: args.abstract,
+                system: args.system,
+            });
+            return formatToolResult({
+                system: args.system,
+                classifications: result[args.system],
+            });
+        }
+        catch (error) {
+            return formatErrorResult(error);
+        }
+    });
+    // Extract Concepts
+    server.registerTool("extract_concepts", {
+        description: "Extract research concepts from text using Dimensions natural language processing. " +
+            "Identifies key scientific concepts, terms, and topics from abstracts or descriptions.",
+        inputSchema: {
+            text: z
+                .string()
+                .min(1)
+                .describe("Text to extract concepts from (e.g., abstract, description)"),
+            return_scores: z
+                .boolean()
+                .optional()
+                .default(false)
+                .describe("Include relevance scores for each concept (0-1 scale)"),
+        },
+        outputSchema: {
+            concepts: z.array(z.record(z.string(), z.unknown())).describe("Extracted concepts"),
+            returnedWithScores: z.boolean().describe("Whether relevance scores are included"),
+        },
+        annotations: READ_ONLY_API_ANNOTATIONS,
+    }, async (args) => {
+        try {
+            const result = await client.extractConcepts(args.text, {
+                returnScores: args.return_scores,
+            });
+            return formatToolResult({
+                concepts: result.extracted_concepts,
+                returnedWithScores: args.return_scores,
+            });
+        }
+        catch (error) {
+            return formatErrorResult(error);
+        }
+    });
+    // Find Similar Publications
+    server.registerTool("find_similar_publications", {
+        description: "Find publications semantically similar to provided text. " +
+            "Uses the similar_documents() function to match publications based on meaning, " +
+            "not just keywords. Great for finding related research based on an abstract.",
+        inputSchema: {
+            text: z
+                .string()
+                .min(1)
+                .describe("Abstract or description text to find similar publications for"),
+            year_from: z
+                .number()
+                .int()
+                .optional()
+                .describe("Filter publications from this year (inclusive)"),
+            year_to: z
+                .number()
+                .int()
+                .optional()
+                .describe("Filter publications up to this year (inclusive)"),
+            limit: z
+                .number()
+                .int()
+                .min(1)
+                .max(1000)
+                .default(10)
+                .describe("Maximum results to return (max 1000)"),
+            fields: z
+                .array(z.string())
+                .optional()
+                .describe("Fields to return (e.g., ['id', 'title', 'doi', 'year', 'times_cited'])"),
+        },
+        outputSchema: {
+            totalCount: z.number().describe("Total matching records"),
+            returnedCount: z.number().describe("Records returned in this response"),
+            publications: z.array(z.record(z.string(), z.unknown())).describe("Similar publications"),
+        },
+        annotations: READ_ONLY_API_ANNOTATIONS,
+    }, withFieldAliases({ entitySource: { kind: "static", entity: "publications" }, fieldArrayArgs: ["fields"] }, async (args) => {
+        try {
+            let builder = client.publications().forSimilar(args.text);
+            if (args.year_from !== undefined) {
+                builder = builder.where("year", ">=", args.year_from);
+            }
+            if (args.year_to !== undefined) {
+                builder = builder.where("year", "<=", args.year_to);
+            }
+            if (args.fields && args.fields.length > 0) {
+                builder = builder.fields(args.fields);
+            }
+            const result = await builder.limit(args.limit).execute();
+            return formatToolResult({
+                totalCount: result.totalCount,
+                returnedCount: result.data.length,
+                publications: result.data,
+            });
+        }
+        catch (error) {
+            return formatErrorResult(error);
+        }
+    }));
+    // Extract Affiliations
+    server.registerTool("extract_affiliations", {
+        description: "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: {
+            affiliations: z
+                .array(z.object({
+                affiliation: z
+                    .string()
+                    .optional()
+                    .describe("Freetext affiliation string (e.g., 'University of Oxford, UK')"),
+                name: z.string().optional().describe("Organization name"),
+                city: z.string().optional().describe("City"),
+                state: z.string().optional().describe("State/province"),
+                country: z.string().optional().describe("Country"),
+            }))
+                .min(1)
+                .describe("Array of affiliations to resolve. Each must have either 'affiliation' or 'name'"),
+        },
+        outputSchema: {
+            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) => {
+        try {
+            const result = await client.extractAffiliations(args.affiliations);
+            return formatToolResult({
+                matchCount: result.extracted_affiliations.length,
+                affiliations: result.extracted_affiliations,
+            });
+        }
+        catch (error) {
+            return formatErrorResult(error);
+        }
+    });
+    // Extract Grants
+    server.registerTool("extract_grants", {
+        description: "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: {
+            grant_number: z.string().min(1).describe("Grant number to look up (e.g., 'R01HL117329')"),
+            fundref: z
+                .string()
+                .optional()
+                .describe("FundRef ID of the funder (e.g., '100000050' for NIH)"),
+            funder_name: z
+                .string()
+                .optional()
+                .describe("Funder name as alternative to FundRef ID (e.g., 'NIH')"),
+        },
+        outputSchema: {
+            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) => {
+        try {
+            const result = await client.extractGrants({
+                grantNumber: args.grant_number,
+                fundref: args.fundref,
+                funderName: args.funder_name,
+            });
+            return formatToolResult({
+                matchCount: result.grant_id ? 1 : 0,
+                grants: result.grant_id ? [{ grant_id: result.grant_id }] : [],
+            });
+        }
+        catch (error) {
+            return formatErrorResult(error);
+        }
+    });
+    // Find Similar Grants
+    server.registerTool("find_similar_grants", {
+        description: "Find grants semantically similar to provided text. " +
+            "Uses the similar_documents() function to match grants based on meaning. " +
+            "Useful for identifying similar funding opportunities or research projects.",
+        inputSchema: {
+            text: z
+                .string()
+                .min(1)
+                .describe("Project description or abstract to find similar grants for"),
+            start_year_from: z
+                .number()
+                .int()
+                .optional()
+                .describe("Filter grants starting from this year (inclusive)"),
+            start_year_to: z
+                .number()
+                .int()
+                .optional()
+                .describe("Filter grants starting up to this year (inclusive)"),
+            limit: z
+                .number()
+                .int()
+                .min(1)
+                .max(1000)
+                .default(10)
+                .describe("Maximum results to return (max 1000)"),
+            fields: z
+                .array(z.string())
+                .optional()
+                .describe("Fields to return (e.g., ['id', 'title', 'funder_org_name', 'funding_usd'])"),
+        },
+        outputSchema: {
+            totalCount: z.number().describe("Total matching records"),
+            returnedCount: z.number().describe("Records returned in this response"),
+            grants: z.array(z.record(z.string(), z.unknown())).describe("Similar grants"),
+        },
+        annotations: READ_ONLY_API_ANNOTATIONS,
+    }, withFieldAliases({ entitySource: { kind: "static", entity: "grants" }, fieldArrayArgs: ["fields"] }, async (args) => {
+        try {
+            let builder = client.grants().forSimilar(args.text);
+            if (args.start_year_from !== undefined) {
+                builder = builder.where("start_year", ">=", args.start_year_from);
+            }
+            if (args.start_year_to !== undefined) {
+                builder = builder.where("start_year", "<=", args.start_year_to);
+            }
+            if (args.fields && args.fields.length > 0) {
+                builder = builder.fields(args.fields);
+            }
+            const result = await builder.limit(args.limit).execute();
+            return formatToolResult({
+                totalCount: result.totalCount,
+                returnedCount: result.data.length,
+                grants: result.data,
+            });
+        }
+        catch (error) {
+            return formatErrorResult(error);
+        }
+    }));
+}
+//# sourceMappingURL=functions.js.map

package/dist/tools/functions.js.map

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package/dist/tools/impact-chain.d.ts

@@ -0,0 +1,15 @@
+/**
+ * Research impact chain tool for the MCP server.
+ * Traces how a research topic flows from publications through patents,
+ * clinical trials, and policy documents.
+ * @module mcp/tools/impact-chain
+ */
+import type { DimensionsClient } from "@digital-science/dimensions-dsl";
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+/**
+ * Registers the research_impact_chain tool with the MCP server.
+ * @param server - MCP server instance
+ * @param client - Dimensions client instance
+ */
+export declare function registerImpactChainTools(server: McpServer, client: DimensionsClient): void;
+//# sourceMappingURL=impact-chain.d.ts.map

package/dist/tools/impact-chain.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"impact-chain.d.ts","sourceRoot":"","sources":["../../src/tools/impact-chain.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,iCAAiC,CAAC;AACxE,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAiCzE;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,gBAAgB,GAAG,IAAI,CAqE1F"}

package/dist/tools/impact-chain.js

@@ -0,0 +1,96 @@
+/**
+ * Research impact chain tool for the MCP server.
+ * Traces how a research topic flows from publications through patents,
+ * clinical trials, and policy documents.
+ * @module mcp/tools/impact-chain
+ */
+import { z } from "zod";
+import { asArray, formatErrorResult, formatToolResult, READ_ONLY_API_ANNOTATIONS, } from "../utils.js";
+/** Impact chain stages in translation order. */
+const CHAIN_STAGES = [
+    {
+        entityType: "publications",
+        fields: ["id", "title", "doi", "year", "times_cited", "journal"],
+        sortField: "year",
+    },
+    {
+        entityType: "patents",
+        fields: ["id", "title", "year", "filing_date", "assignees"],
+        sortField: "year",
+    },
+    {
+        entityType: "clinical_trials",
+        fields: ["id", "title", "phase", "overall_status", "conditions"],
+        sortField: "date_inserted",
+    },
+    {
+        entityType: "policy_documents",
+        fields: ["id", "title", "year", "publisher_org"],
+        sortField: "year",
+    },
+];
+/**
+ * Registers the research_impact_chain tool with the MCP server.
+ * @param server - MCP server instance
+ * @param client - Dimensions client instance
+ */
+export function registerImpactChainTools(server, client) {
+    server.registerTool("research_impact_chain", {
+        description: "Trace how a research topic translates from basic science through real-world impact. Shows publications, patents, clinical trials, and policy documents for a query.",
+        inputSchema: {
+            query: z.string().describe("Seed topic or concept (e.g., 'gene therapy', 'CRISPR')"),
+            entityLimit: z.number().int().min(1).max(50).default(10).describe("Max entities per stage"),
+        },
+        outputSchema: {
+            found: z.boolean().describe("Whether results were found"),
+            query: z.string().optional().describe("The seed query"),
+            profile: z
+                .record(z.string(), z.unknown())
+                .optional()
+                .describe("Impact chain profile with stages"),
+        },
+        annotations: READ_ONLY_API_ANNOTATIONS,
+    }, async (args) => {
+        try {
+            const profile = {};
+            const stageResults = await Promise.all(CHAIN_STAGES.map(async (stage) => {
+                const builder = client
+                    .createQueryBuilder()
+                    .search(stage.entityType)
+                    .for(args.query)
+                    .fields([...stage.fields])
+                    .sort(stage.sortField, "desc")
+                    .limit(args.entityLimit);
+                const dsl = builder.build();
+                const response = await client.rawQuery(dsl);
+                const items = asArray(response[stage.entityType]);
+                return {
+                    entityType: stage.entityType,
+                    totalCount: typeof response._stats?.total_count === "number"
+                        ? response._stats.total_count
+                        : items.length,
+                    returnedCount: items.length,
+                    items,
+                };
+            }));
+            const stages = {};
+            for (const result of stageResults) {
+                stages[result.entityType] = {
+                    totalCount: result.totalCount,
+                    returnedCount: result.returnedCount,
+                    items: result.items,
+                };
+            }
+            profile.stages = stages;
+            return formatToolResult({
+                found: true,
+                query: args.query,
+                profile,
+            });
+        }
+        catch (error) {
+            return formatErrorResult(error);
+        }
+    });
+}
+//# sourceMappingURL=impact-chain.js.map

package/dist/tools/impact-chain.js.map

@@ -0,0 +1 @@
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