npm - @cyanheads/ensembl-mcp-server - Versions diffs - 0.2.0 → 0.3.0 - Mend

@cyanheads/ensembl-mcp-server 0.2.0 → 0.3.0

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Files changed (23) hide show

package/AGENTS.md +3 -3
package/CLAUDE.md +3 -3
package/README.md +5 -4
package/changelog/0.3.x/0.3.0.md +26 -0
package/dist/index.js +7 -2
package/dist/index.js.map +1 -1
package/dist/mcp-server/resources/definitions/species.resource.d.ts +7 -4
package/dist/mcp-server/resources/definitions/species.resource.d.ts.map +1 -1
package/dist/mcp-server/resources/definitions/species.resource.js +46 -21
package/dist/mcp-server/resources/definitions/species.resource.js.map +1 -1
package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts.map +1 -1
package/dist/mcp-server/tools/definitions/get-homology.tool.js +14 -8
package/dist/mcp-server/tools/definitions/get-homology.tool.js.map +1 -1
package/dist/mcp-server/tools/definitions/list-species.tool.js +4 -4
package/dist/mcp-server/tools/definitions/list-species.tool.js.map +1 -1
package/dist/services/ensembl/ensembl-service.d.ts +3 -3
package/dist/services/ensembl/ensembl-service.d.ts.map +1 -1
package/dist/services/ensembl/ensembl-service.js +7 -3
package/dist/services/ensembl/ensembl-service.js.map +1 -1
package/dist/services/ensembl/types.d.ts +11 -0
package/dist/services/ensembl/types.d.ts.map +1 -1
package/package.json +2 -2
package/server.json +3 -3

package/AGENTS.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Developer Protocol
 **Server:** ensembl-mcp-server
-**Version:** 0.2.0
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
+**Version:** 0.3.0
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
 **Zod:** ^4.4.3
@@ -225,7 +225,7 @@ src/
     resources/definitions/
       gene.resource.ts                  # ensembl://gene/{id}
       transcript.resource.ts            # ensembl://transcript/{id}
-      species.resource.ts               # ensembl://species
+      species.resource.ts               # ensembl://species, ensembl://species/{division}
     prompts/definitions/
       gene-dossier.prompt.ts            # ensembl_gene_dossier workflow prompt
 ```

package/CLAUDE.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Developer Protocol
 **Server:** ensembl-mcp-server
-**Version:** 0.2.0
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
+**Version:** 0.3.0
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
 **Zod:** ^4.4.3
@@ -225,7 +225,7 @@ src/
     resources/definitions/
       gene.resource.ts                  # ensembl://gene/{id}
       transcript.resource.ts            # ensembl://transcript/{id}
-      species.resource.ts               # ensembl://species
+      species.resource.ts               # ensembl://species, ensembl://species/{division}
     prompts/definitions/
       gene-dossier.prompt.ts            # ensembl_gene_dossier workflow prompt
 ```

package/README.md CHANGED Viewed

@@ -1,13 +1,13 @@
 <div align="center">
   <h1>@cyanheads/ensembl-mcp-server</h1>
   <p><b>Look up genes, fetch sequences, predict variant consequences, find orthologs and cross-database xrefs via Ensembl REST via MCP. STDIO or Streamable HTTP.</b>
-  <div>7 Tools • 3 Resources • 1 Prompt</div>
+  <div>7 Tools • 4 Resources • 1 Prompt</div>
   </p>
 </div>
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.2.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/ensembl-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [![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-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.3.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/ensembl-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [![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-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -122,10 +122,11 @@ Full cross-database reference set for any Ensembl feature.
 |:-----|:-----|:------------|
 | Resource | `ensembl://gene/{id}` | Gene record by stable ID (`ENSG…`) — location, biotype, description, and transcript list |
 | Resource | `ensembl://transcript/{id}` | Transcript record by stable ID (`ENST…`) — parent gene, location, biotype, canonical flag, and length |
-| Resource | `ensembl://species` | Full list of supported Ensembl species with name, display name, assembly, taxon ID, and division |
+| Resource | `ensembl://species` | Supported Ensembl species for the endpoint default division (vertebrates on the default endpoint) with name, display name, assembly, taxon ID, and division |
+| Resource | `ensembl://species/{division}` | Supported species in one division (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`) |
 | Prompt | `ensembl_gene_dossier` | Structured workflow for assembling a complete gene profile: symbol → ID + location → sequence → variants → orthologs → xrefs |
-All resource data is also reachable via tools. The `ensembl://species` resource provides the full species catalog with cursor pagination; `ensembl_list_species` is the tool equivalent with filtering support.
+All resource data is also reachable via tools. `ensembl://species` returns the endpoint default division (vertebrates) and `ensembl://species/{division}` returns a named division; `ensembl_list_species` is the tool equivalent, filtering by division and name.
 ## Features

package/changelog/0.3.x/0.3.0.md ADDED Viewed

@@ -0,0 +1,26 @@
+---
+summary: "Adds a division-addressable ensembl://species/{division} resource; ensembl_get_homology symbol queries now return the resolved Ensembl stable gene ID as queryId; mcp-ts-core 0.10.10 clears 7 transitive vulnerabilities (bun audit 7 → 0)"
+breaking: false
+security: true
+---
+# 0.3.0 — 2026-07-03
+## Added
+- **`ensembl://species/{division}` resource** — division-addressable counterpart to `ensembl://species`, templated by `division` (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`). `list()` enumerates one addressable URI per division. ([#8](https://github.com/cyanheads/ensembl-mcp-server/issues/8))
+## Changed
+- **`ensembl_get_homology` symbol-mode `queryId` now returns the resolved Ensembl stable gene ID** — previously echoed the submitted symbol verbatim; now surfaces the stable ID from the upstream response's `data[].id` entry, falling back to the submitted symbol/ID only when the response carries no data entry. Gives callers a chainable ID instead of an opaque symbol. ([#6](https://github.com/cyanheads/ensembl-mcp-server/issues/6))
+- **`ensembl://species` drops its `division` filter param** — the param was unreachable (a static URI has no template variable to populate it). The resource now always returns the endpoint default division (vertebrates on the default GRCh38 endpoint); read `ensembl://species/{division}` for a named division. ([#8](https://github.com/cyanheads/ensembl-mcp-server/issues/8))
+- **`ensembl_list_species` description corrected** — no longer claims omitting `division` returns all divisions; states it returns the endpoint default division (vertebrates). ([#12](https://github.com/cyanheads/ensembl-mcp-server/issues/12))
+- **`@cyanheads/mcp-ts-core`** `^0.10.9` → `^0.10.10`
+## Security
+`bun audit`: 7 vulnerabilities → 0, via the `mcp-ts-core` `^0.10.10` lockfile re-resolve:
+- **js-yaml** `3.14.2` → `3.15.0` — quadratic-complexity DoS in merge-key handling via repeated aliases ([GHSA-h67p-54hq-rp68](https://github.com/advisories/GHSA-h67p-54hq-rp68), moderate)
+- **hono** — the SDK's separately-resolved `hono@4.12.23` collapses onto the shared, already-safe `4.12.27` resolution, clearing 5 advisories fixed at `4.12.25`+: CORS reflects any Origin with credentials on a wildcard default ([GHSA-88fw-hqm2-52qc](https://github.com/advisories/GHSA-88fw-hqm2-52qc), high), plus 4 moderate Lambda/Lambda@Edge/`serve-static` advisories (Set-Cookie merging, body-limit bypass, header dropping, Windows path traversal)
+- **esbuild** `0.28.0` (dev-only, pulled in transitively via `tsx`) drops out of the tree entirely, clearing a Windows dev-server arbitrary-file-read advisory ([GHSA-g7r4-m6w7-qqqr](https://github.com/advisories/GHSA-g7r4-m6w7-qqqr), low)

package/dist/index.js CHANGED Viewed

@@ -6,7 +6,7 @@
 import { createApp } from '@cyanheads/mcp-ts-core';
 import { ensemblGeneDossierPrompt } from './mcp-server/prompts/definitions/gene-dossier.prompt.js';
 import { ensemblGeneResource } from './mcp-server/resources/definitions/gene.resource.js';
-import { ensemblSpeciesResource } from './mcp-server/resources/definitions/species.resource.js';
+import { ensemblSpeciesByDivisionResource, ensemblSpeciesResource, } from './mcp-server/resources/definitions/species.resource.js';
 import { ensemblTranscriptResource } from './mcp-server/resources/definitions/transcript.resource.js';
 import { ensemblGetHomology } from './mcp-server/tools/definitions/get-homology.tool.js';
 import { ensemblGetSequence } from './mcp-server/tools/definitions/get-sequence.tool.js';
@@ -28,7 +28,12 @@ await createApp({
         ensemblGetHomology,
         ensemblGetXrefs,
     ],
-    resources: [ensemblGeneResource, ensemblTranscriptResource, ensemblSpeciesResource],
+    resources: [
+        ensemblGeneResource,
+        ensemblTranscriptResource,
+        ensemblSpeciesResource,
+        ensemblSpeciesByDivisionResource,
+    ],
     prompts: [ensemblGeneDossierPrompt],
     instructions: `Ensembl genomics server — vertebrate and model organism gene, sequence, and variant data.
 Species names use Ensembl internal format: lowercase_underscore scientific names (homo_sapiens, mus_musculus).

package/dist/index.js.map CHANGED Viewed

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package/dist/mcp-server/resources/definitions/species.resource.d.ts CHANGED Viewed

@@ -1,15 +1,18 @@
 /**
- * @fileoverview Resource exposing the Ensembl species catalog.
+ * @fileoverview Resources exposing the Ensembl species catalog — the endpoint
+ * default division (vertebrates) at `ensembl://species` and a division-filtered
+ * view at the `ensembl://species/{division}` template.
  * @module mcp-server/resources/definitions/species
  */
 import { z } from '@cyanheads/mcp-ts-core';
-export declare const ensemblSpeciesResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
-    division: z.ZodOptional<z.ZodEnum<{
+export declare const ensemblSpeciesResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{}, z.core.$strip>, undefined, undefined>;
+export declare const ensemblSpeciesByDivisionResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
+    division: z.ZodEnum<{
         EnsemblVertebrates: "EnsemblVertebrates";
         EnsemblPlants: "EnsemblPlants";
         EnsemblFungi: "EnsemblFungi";
         EnsemblMetazoa: "EnsemblMetazoa";
         EnsemblProtists: "EnsemblProtists";
-    }>>;
+    }>;
 }, z.core.$strip>, undefined, undefined>;
 //# sourceMappingURL=species.resource.d.ts.map

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package/dist/mcp-server/resources/definitions/species.resource.js CHANGED Viewed

@@ -1,5 +1,7 @@
 /**
- * @fileoverview Resource exposing the Ensembl species catalog.
+ * @fileoverview Resources exposing the Ensembl species catalog — the endpoint
+ * default division (vertebrates) at `ensembl://species` and a division-filtered
+ * view at the `ensembl://species/{division}` template.
  * @module mcp-server/resources/definitions/species
  */
 import { resource, z } from '@cyanheads/mcp-ts-core';
@@ -11,38 +13,61 @@ const DIVISION_VALUES = [
     'EnsemblMetazoa',
     'EnsemblProtists',
 ];
+/** Fetch the species catalog (optionally filtered to one division), sorted by internal name. */
+async function loadSpeciesCatalog(division, ctx) {
+    const service = getEnsemblService();
+    const species = await service.listSpecies(division, ctx);
+    species.sort((a, b) => a.name.localeCompare(b.name));
+    return { species, totalCount: species.length };
+}
 export const ensemblSpeciesResource = resource('ensembl://species', {
     name: 'Ensembl Species',
-    description: 'Complete catalog of Ensembl-supported species with internal name, display name, assembly, ' +
-        'taxon ID, and division. Addressable reference for tool bootstrapping. ' +
-        'Contains ~350 vertebrate species plus additional non-vertebrate divisions. ' +
-        'Use this as stable, injectable context when working with unfamiliar species names.',
+    description: 'Ensembl species catalog for the endpoint default division — internal name, display name, assembly, ' +
+        'taxon ID, and division. On the default GRCh38 endpoint this returns the vertebrate division (~356 species). ' +
+        'Stable, injectable context for unfamiliar species names. ' +
+        'For a specific division read ensembl://species/{division} (e.g. ensembl://species/EnsemblPlants); ' +
+        'the ensembl_list_species tool also filters by division and name.',
     mimeType: 'application/json',
-    params: z.object({
-        division: z
-            .enum(DIVISION_VALUES)
-            .optional()
-            .describe('Filter to a specific Ensembl division. ' + 'Omit to return species from all divisions.'),
-    }),
-    async handler(params, ctx) {
-        ctx.log.debug('Fetching species resource', { division: params.division });
-        const service = getEnsemblService();
-        const allSpecies = await service.listSpecies(params.division, ctx);
-        allSpecies.sort((a, b) => a.name.localeCompare(b.name));
-        return {
-            species: allSpecies,
-            totalCount: allSpecies.length,
-        };
+    params: z.object({}),
+    async handler(_params, ctx) {
+        ctx.log.debug('Fetching species resource (endpoint default division)');
+        return await loadSpeciesCatalog(undefined, ctx);
     },
     list: async () => ({
         resources: [
             {
                 uri: 'ensembl://species',
                 name: 'All Ensembl Species',
-                description: 'Complete catalog of Ensembl-supported species',
+                description: 'Ensembl species for the endpoint default division (vertebrates by default)',
                 mimeType: 'application/json',
             },
         ],
     }),
 });
+export const ensemblSpeciesByDivisionResource = resource('ensembl://species/{division}', {
+    name: 'Ensembl Species by Division',
+    description: 'Ensembl-supported species within a single division (EnsemblVertebrates, EnsemblPlants, EnsemblFungi, ' +
+        'EnsemblMetazoa, or EnsemblProtists) — internal name, display name, assembly, taxon ID, and division. ' +
+        'Read ensembl://species for the endpoint default division (vertebrates), or use the ensembl_list_species ' +
+        'tool to also filter by name.',
+    mimeType: 'application/json',
+    params: z.object({
+        division: z
+            .enum(DIVISION_VALUES)
+            .describe('Ensembl division to filter to. One of EnsemblVertebrates, EnsemblPlants, EnsemblFungi, ' +
+            'EnsemblMetazoa, EnsemblProtists.'),
+    }),
+    async handler(params, ctx) {
+        ctx.log.debug('Fetching species resource by division', { division: params.division });
+        return await loadSpeciesCatalog(params.division, ctx);
+    },
+    list: async () => ({
+        resources: DIVISION_VALUES.map((division) => ({
+            uri: `ensembl://species/${division}`,
+            name: `${division} species`,
+            description: `Ensembl-supported species in the ${division} division`,
+            mimeType: 'application/json',
+        })),
+    }),
+});
 //# sourceMappingURL=species.resource.js.map

package/dist/mcp-server/resources/definitions/species.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"species.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/species.resource.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAGH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,eAAe,GAAG;IACtB,oBAAoB;IACpB,eAAe;IACf,cAAc;IACd,gBAAgB;IAChB,iBAAiB;CACT,CAAC;AAEX,gGAAgG;AAChG,KAAK,UAAU,kBAAkB,CAAC,QAA4B,EAAE,GAAY;IAC1E,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;IACpC,MAAM,OAAO,GAAG,MAAM,OAAO,CAAC,WAAW,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;IACzD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;IACrD,OAAO,EAAE,OAAO,EAAE,UAAU,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC;AACjD,CAAC;AAED,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,mBAAmB,EAAE;IAClE,IAAI,EAAE,iBAAiB;IACvB,WAAW,EACT,qGAAqG;QACrG,8GAA8G;QAC9G,2DAA2D;QAC3D,oGAAoG;QACpG,kEAAkE;IACpE,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC;IAEpB,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG;QACxB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,uDAAuD,CAAC,CAAC;QACvE,OAAO,MAAM,kBAAkB,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;IAClD,CAAC;IAED,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,mBAAmB;gBACxB,IAAI,EAAE,qBAAqB;gBAC3B,WAAW,EAAE,4EAA4E;gBACzF,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,gCAAgC,GAAG,QAAQ,CAAC,8BAA8B,EAAE;IACvF,IAAI,EAAE,6BAA6B;IACnC,WAAW,EACT,uGAAuG;QACvG,uGAAuG;QACvG,0GAA0G;QAC1G,8BAA8B;IAChC,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,IAAI,CAAC,eAAe,CAAC;aACrB,QAAQ,CACP,yFAAyF;YACvF,kCAAkC,CACrC;KACJ,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,uCAAuC,EAAE,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC;QACtF,OAAO,MAAM,kBAAkB,CAAC,MAAM,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;IACxD,CAAC;IAED,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE,eAAe,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC;YAC5C,GAAG,EAAE,qBAAqB,QAAQ,EAAE;YACpC,IAAI,EAAE,GAAG,QAAQ,UAAU;YAC3B,WAAW,EAAE,oCAAoC,QAAQ,WAAW;YACpE,QAAQ,EAAE,kBAAkB;SAC7B,CAAC,CAAC;KACJ,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-homology.tool.js CHANGED Viewed

@@ -127,29 +127,35 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
         let queryId;
         let homologs;
         if (idTrimmed) {
-            queryId = idTrimmed;
-            homologs = await service
-                .getHomologyById(queryId, input.species, input.type, input.target_species, ctx)
+            const result = await service
+                .getHomologyById(idTrimmed, input.species, input.type, input.target_species, ctx)
                 .catch((err) => {
                 const msg = err instanceof Error ? err.message : String(err);
                 if (/not found|no valid lookup|page not found/i.test(msg)) {
-                    throw ctx.fail('not_found', `Gene ID "${queryId}" not found in Ensembl.`);
+                    throw ctx.fail('not_found', `Gene ID "${idTrimmed}" not found in Ensembl.`);
                 }
                 throw err;
             });
+            homologs = result.homologs;
+            // Prefer the stable ID the upstream resolved the query to; fall back to the submitted ID.
+            queryId = result.resolvedQueryId ?? idTrimmed;
         }
         else {
-            queryId = symbolTrimmed ?? '';
-            homologs = await service
-                .getHomologyBySymbol(queryId, input.species, input.type, input.target_species, ctx)
+            const submittedSymbol = symbolTrimmed ?? '';
+            const result = await service
+                .getHomologyBySymbol(submittedSymbol, input.species, input.type, input.target_species, ctx)
                 .catch((err) => {
                 const msg = err instanceof Error ? err.message : String(err);
                 // Ensembl returns {"error":"<species_name>"} for invalid gene symbols in homology endpoint
                 if (/not found|no valid lookup/i.test(msg) || msg === input.species) {
-                    throw ctx.fail('not_found', `Gene symbol "${queryId}" not found in ${input.species}.`);
+                    throw ctx.fail('not_found', `Gene symbol "${submittedSymbol}" not found in ${input.species}.`);
                 }
                 throw err;
             });
+            homologs = result.homologs;
+            // Surface the resolved Ensembl stable gene ID rather than echoing the symbol (#6);
+            // fall back to the submitted symbol only when the response carried no data entry.
+            queryId = result.resolvedQueryId ?? submittedSymbol;
         }
         if (homologs.length === 0) {
             ctx.enrich.notice(`No ${input.type} found for "${queryId}" in ${input.species}` +

package/dist/mcp-server/tools/definitions/get-homology.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/mcp-server/tools/definitions/list-species.tool.js CHANGED Viewed

@@ -32,9 +32,9 @@ export const ensemblListSpecies = tool('ensembl_list_species', {
     title: 'List Ensembl Species',
     description: 'List species supported by Ensembl with display name, common name, assembly, taxon ID, and division. ' +
         'Required discovery step — species names like homo_sapiens are opaque to non-biologists and are the ' +
-        'input format every other Ensembl tool expects. Filter by division to limit results; use nameContains ' +
-        'to find a species by partial name match. Returns the full species catalog when no filters are applied ' +
-        '(EnsemblVertebrates has ~250 species; all divisions combined have ~1,000+).',
+        'input format every other Ensembl tool expects. Filter by division to select one; use nameContains ' +
+        'to find a species by partial name match. With no division, returns the endpoint default division — ' +
+        'the vertebrates (~356 species on the default GRCh38 endpoint); pass a division to list that division.',
     annotations: { readOnlyHint: true, openWorldHint: false, idempotentHint: true },
     input: z.object({
         division: z
@@ -44,7 +44,7 @@ export const ensemblListSpecies = tool('ensembl_list_species', {
             'EnsemblVertebrates includes human, mouse, zebrafish, and other vertebrates. ' +
             'EnsemblPlants covers crop and model plant genomes. ' +
             'EnsemblFungi, EnsemblMetazoa, EnsemblProtists cover non-vertebrate model organisms. ' +
-            'Omit to return all divisions.'),
+            'Omit to return the endpoint default division (vertebrates).'),
         nameContains: z
             .string()
             .optional()

package/dist/mcp-server/tools/definitions/list-species.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ensembl/ensembl-service.d.ts CHANGED Viewed

@@ -6,7 +6,7 @@
 import type { Context } from '@cyanheads/mcp-ts-core';
 import type { AppConfig } from '@cyanheads/mcp-ts-core/config';
 import type { StorageService } from '@cyanheads/mcp-ts-core/storage';
-import type { GeneRecord, HomologyEntry, OverlapFeature, SequenceRecord, SpeciesInfo, TranscriptRecord, VepRecord, XrefEntry } from './types.js';
+import type { GeneRecord, HomologyResult, OverlapFeature, SequenceRecord, SpeciesInfo, TranscriptRecord, VepRecord, XrefEntry } from './types.js';
 export declare class EnsemblService {
     private readonly baseUrl;
     constructor(_config: AppConfig, _storage: StorageService);
@@ -22,8 +22,8 @@ export declare class EnsemblService {
     queryRegion(species: string, region: string, features: string[], biotype: string | undefined, ctx: Context): Promise<OverlapFeature[]>;
     predictVariantHgvs(notation: string, species: string, ctx: Context): Promise<VepRecord[]>;
     predictVariantRegion(chr: string, start: number, end: number, strand: number, allele: string, species: string, ctx: Context): Promise<VepRecord[]>;
-    getHomologyBySymbol(symbol: string, species: string, type: string, targetSpecies: string | undefined, ctx: Context): Promise<HomologyEntry[]>;
-    getHomologyById(id: string, species: string, type: string, targetSpecies: string | undefined, ctx: Context): Promise<HomologyEntry[]>;
+    getHomologyBySymbol(symbol: string, species: string, type: string, targetSpecies: string | undefined, ctx: Context): Promise<HomologyResult>;
+    getHomologyById(id: string, species: string, type: string, targetSpecies: string | undefined, ctx: Context): Promise<HomologyResult>;
     getXrefsById(id: string, dbname: string | undefined, ctx: Context): Promise<XrefEntry[]>;
     listSpecies(division: string | undefined, ctx: Context): Promise<SpeciesInfo[]>;
 }

package/dist/services/ensembl/ensembl-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ensembl/ensembl-service.js CHANGED Viewed

@@ -111,9 +111,7 @@ function normalizeVep(raw) {
 }
 function normalizeHomology(raw, sourceId) {
     const dataEntry = raw.data?.find((d) => d.id === sourceId) ?? raw.data?.[0];
-    if (!dataEntry?.homologies)
-        return [];
-    return dataEntry.homologies.map((h) => ({
+    const homologs = (dataEntry?.homologies ?? []).map((h) => ({
         targetId: h.target?.id ?? h.id,
         ...(h.target?.species
             ? { targetSpecies: h.target.species }
@@ -129,6 +127,12 @@ function normalizeHomology(raw, sourceId) {
         }),
         ...(h.taxonomy_level && { taxonomyLevel: h.taxonomy_level }),
     }));
+    // dataEntry.id is the Ensembl stable gene ID the query resolved to — surface it
+    // so symbol-mode callers get a chainable stable ID, not the echoed symbol.
+    return {
+        homologs,
+        ...(dataEntry?.id && { resolvedQueryId: dataEntry.id }),
+    };
 }
 function normalizeXref(raw) {
     return {

package/dist/services/ensembl/ensembl-service.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ensembl/types.d.ts CHANGED Viewed

@@ -271,6 +271,17 @@ export type HomologyEntry = {
     percPos?: number;
     taxonomyLevel?: string;
 };
+/**
+ * Homology lookup result. `resolvedQueryId` is the Ensembl stable gene ID the
+ * upstream response matched the query to (from the `data[].id` entry) — present
+ * for both symbol- and ID-mode queries, absent only when the response carries no
+ * data entry. Lets the tool surface a stable, chainable `queryId` even when the
+ * caller queried by symbol.
+ */
+export type HomologyResult = {
+    homologs: HomologyEntry[];
+    resolvedQueryId?: string;
+};
 export type XrefEntry = {
     dbname?: string;
     dbDisplayName?: string;

package/dist/services/ensembl/types.d.ts.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/ensembl-mcp-server",
-  "version": "0.2.0",
+  "version": "0.3.0",
   "mcpName": "io.github.cyanheads/ensembl-mcp-server",
   "description": "Look up genes, fetch sequences, predict variant consequences, find orthologs and cross-database xrefs via Ensembl REST via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -90,7 +90,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.10.9",
+    "@cyanheads/mcp-ts-core": "^0.10.10",
     "pino-pretty": "^13.1.3",
     "zod": "^4.4.3"
   },

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/ensembl-mcp-server",
     "source": "github"
   },
-  "version": "0.2.0",
+  "version": "0.3.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/ensembl-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.2.0",
+      "version": "0.3.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -55,7 +55,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/ensembl-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.2.0",
+      "version": "0.3.0",
       "packageArguments": [
         {
           "type": "positional",