npm - @cyanheads/ensembl-mcp-server - Versions diffs - 0.3.0 → 0.4.0 - Mend

@cyanheads/ensembl-mcp-server 0.3.0 → 0.4.0

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Files changed (22) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** ensembl-mcp-server
-**Version:** 0.3.0
+**Version:** 0.4.0
 **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

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** ensembl-mcp-server
-**Version:** 0.3.0
+**Version:** 0.4.0
 **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

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![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/)
+[![Version](https://img.shields.io/badge/Version-0.4.0-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>

package/changelog/0.4.x/0.4.0.md ADDED Viewed

@@ -0,0 +1,20 @@
+---
+summary: "ensembl_predict_variant accepts dbSNP rsIDs via a new VEP /id endpoint; ensembl_query_region exon rows carry parentId/rank; chromosome-name docs corrected; gene-dossier prompt's variant workflow now attributes impact to VEP"
+breaking: false
+security: false
+---
+# 0.4.0 — 2026-07-03
+## Added
+- **`ensembl_predict_variant` accepts dbSNP rsIDs** — third input format alongside HGVS and region+allele (e.g. `rs334`), routed to a new VEP `GET /vep/{species}/id/{id}` endpoint via the new `predictVariantId` service method. An rsID unknown to dbSNP surfaces as `not_found`; a malformed identifier as `invalid_notation`. ([#11](https://github.com/cyanheads/ensembl-mcp-server/issues/11))
+- **`ensembl_query_region` exon features carry `parentId` and `rank`** — `parentId` (the `ENST…` parent transcript stable ID) and `rank` (1-based exon position within that transcript) explain why the same exon ID can appear on multiple rows: once per parent transcript it belongs to. ([#9](https://github.com/cyanheads/ensembl-mcp-server/issues/9))
+## Changed
+- **Chromosome-name guidance corrected** in `ensembl_query_region` and `ensembl_predict_variant` (descriptions, input schemas, error recovery text, and the empty-result notice) — no longer states chr-prefixed names are unsupported. Ensembl normalizes chromosome names; canonical vertebrate output omits the `chr` prefix, but a `chr`-prefixed name (e.g. `chr13`) is also accepted. ([#10](https://github.com/cyanheads/ensembl-mcp-server/issues/10))
+## Fixed
+- **`ensembl_gene_dossier` prompt's variant workflow corrected** — step 3 no longer claims `ensembl_query_region` can identify HIGH/MODERATE impact variants (query_region doesn't report functional impact); step 4 now attributes impact to VEP and offers a valid rsID example (`rs334`), consistent with the new rsID input support. ([#7](https://github.com/cyanheads/ensembl-mcp-server/issues/7))

package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"gene-dossier.prompt.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/prompts/definitions/gene-dossier.prompt.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAU,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEnD,eAAO,MAAM,wBAAwB;;;kBA8DnC,CAAC"}

package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.js CHANGED Viewed

@@ -33,9 +33,12 @@ export const ensemblGeneDossierPrompt = prompt('ensembl_gene_dossier', {
                     `transcript ID from step 1 and type="protein". Record the amino acid sequence and its length.\n\n` +
                     `3. **Find variants in the locus** — call \`ensembl_query_region\` with ` +
                     `species="${args.species}", the gene's chromosomal region (chr:start-end from step 1), ` +
-                    `and feature=["variation"]. Identify any HIGH or MODERATE impact variants.\n\n` +
-                    `4. **Predict variant consequences** — for up to 3 high-impact variants found in step 3, ` +
-                    `call \`ensembl_predict_variant\` with the variant ID or HGVS notation. ` +
+                    `and feature=["variation"]. Record the variant IDs (rsIDs), positions, consequence type, ` +
+                    `and any clinical significance. Functional impact (HIGH/MODERATE/LOW) is not reported by ` +
+                    `this step — it comes from VEP in step 4.\n\n` +
+                    `4. **Predict variant consequences** — for up to 3 variants from step 3, ` +
+                    `call \`ensembl_predict_variant\` with each variant's rsID (e.g. rs334), HGVS notation, ` +
+                    `or region+allele. This step returns the functional impact. ` +
                     `Record most_severe_consequence, impact, and clinical significance.\n\n` +
                     `5. **Find cross-species orthologs** — call \`ensembl_get_homology\` with ` +
                     `symbol="${args.gene_symbol}", species="${args.species}", and type="orthologues". ` +

package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.js.map CHANGED Viewed

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

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

@@ -90,22 +90,25 @@ const VepResultSchema = z.object({
 export const ensemblPredictVariant = tool('ensembl_predict_variant', {
     title: 'Predict Variant Effect',
     description: 'Predict the functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP). ' +
-        'Accepts HGVS notation (transcript-relative, e.g. ENST00000380152.8:c.2T>A, or genomic, ' +
-        'e.g. 13:g.32316462T>A) and also region+allele format (chr:start:end:strand/allele, ' +
-        'e.g. 1:65568:65568:1/T). Returns the most severe consequence term, affected transcripts and genes, ' +
+        'Accepts three input formats: HGVS notation (transcript-relative, e.g. ENST00000380152.8:c.2T>A, ' +
+        'or genomic, e.g. 13:g.32316462T>A); region+allele (chr:start:end:strand/allele, e.g. 1:65568:65568:1/T); ' +
+        'and a dbSNP rsID (e.g. rs334). Returns the most severe consequence term, affected transcripts and genes, ' +
         'impact level (HIGH/MODERATE/LOW/MODIFIER), and any colocated known variants with clinical significance. ' +
         'HGVS input: provide the full notation including transcript version for best results. ' +
-        'Region+allele input: use Ensembl chromosome naming (no chr prefix for vertebrates).',
+        'Region+allele input: Ensembl normalizes chromosome names and canonical vertebrate output omits the chr ' +
+        'prefix (a chr-prefixed name is also accepted).',
     annotations: { readOnlyHint: true, openWorldHint: true, idempotentHint: true },
     input: z.object({
         variant: z
             .string()
-            .describe('Variant in one of two formats: ' +
+            .describe('Variant in one of three formats: ' +
             '(1) HGVS notation — transcript-relative: ENST00000380152.8:c.2T>A; ' +
             'genomic: 13:g.32316462T>A; ' +
-            '(2) Region+allele: chr:start:end:strand/allele — e.g. 1:65568:65568:1/T. ' +
-            'For region+allele, strand is 1 (forward) or -1 (reverse); ' +
-            'chromosome names use no "chr" prefix for vertebrates.'),
+            '(2) Region+allele: chr:start:end:strand/allele — e.g. 1:65568:65568:1/T ' +
+            '(strand is 1 for forward or -1 for reverse); ' +
+            '(3) dbSNP rsID — e.g. rs334. ' +
+            'Ensembl normalizes chromosome names; canonical vertebrate output omits the "chr" prefix, ' +
+            'though a chr-prefixed name is also accepted.'),
         species: z
             .string()
             .default('homo_sapiens')
@@ -128,9 +131,8 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
             reason: 'invalid_notation',
             code: JsonRpcErrorCode.ValidationError,
             when: 'The variant notation is malformed or cannot be parsed by VEP.',
-            recovery: 'Check HGVS format: transcript-relative uses ENST…:c.POSREF>ALT; ' +
-                'genomic uses CHR:g.POSREF>ALT. ' +
-                'Region+allele format is chr:start:end:strand/allele. ' +
+            recovery: 'Provide HGVS (transcript-relative ENST…:c.POSREF>ALT or genomic CHR:g.POSREF>ALT), ' +
+                'region+allele (chr:start:end:strand/allele), or a dbSNP rsID (e.g. rs334). ' +
                 'Verify the transcript version matches the current Ensembl release.',
         },
         {
@@ -144,8 +146,10 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
     async handler(input, ctx) {
         ctx.log.info('Predicting variant effect', { variant: input.variant, species: input.species });
         const service = getEnsemblService();
-        // Detect region+allele format: chr:start:end:strand/allele
+        // Route by input format: region+allele (chr:start:end:strand/allele) → /region;
+        // else a dbSNP rsID (rs followed by digits) → /id; else HGVS notation → /hgvs.
         const regionAllelePattern = /^([^:]+):(\d+):(\d+):(-?1)\/(.+)$/;
+        const rsIdPattern = /^rs\d+$/i;
         const regionMatch = input.variant.match(regionAllelePattern);
         let results;
         if (regionMatch) {
@@ -163,6 +167,21 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
                 throw err;
             });
         }
+        else if (rsIdPattern.test(input.variant)) {
+            results = await service
+                .predictVariantId(input.variant, input.species, ctx)
+                .catch((err) => {
+                const msg = err instanceof Error ? err.message : String(err);
+                // A well-formed rsID that dbSNP does not know reports "No variant found with ID …".
+                if (/not found|no variant|unknown variant/i.test(msg)) {
+                    throw ctx.fail('not_found', `Variant identifier ${input.variant} not found in dbSNP.`);
+                }
+                if (/invalid|unrecognized|parse|malformed/i.test(msg)) {
+                    throw ctx.fail('invalid_notation', `Invalid variant identifier "${input.variant}": ${msg}`);
+                }
+                throw err;
+            });
+        }
         else {
             results = await service
                 .predictVariantHgvs(input.variant, input.species, ctx)

package/dist/mcp-server/tools/definitions/predict-variant.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/query-region.tool.d.ts CHANGED Viewed

@@ -8,11 +8,11 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
     species: z.ZodString;
     region: z.ZodString;
     feature: z.ZodDefault<z.ZodArray<z.ZodEnum<{
+        exon: "exon";
         gene: "gene";
         transcript: "transcript";
         variation: "variation";
         regulatory: "regulatory";
-        exon: "exon";
     }>>>;
     biotype: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, z.ZodObject<{
@@ -28,6 +28,8 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
         description: z.ZodOptional<z.ZodString>;
         consequenceType: z.ZodOptional<z.ZodString>;
         clinicalSignificance: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        parentId: z.ZodOptional<z.ZodString>;
+        rank: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     totalCount: z.ZodNumber;
     region: z.ZodString;

package/dist/mcp-server/tools/definitions/query-region.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AA8BjE~~,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+J7B~~,CAAC"}
1	+ {"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwK7B,CAAC"}

package/dist/mcp-server/tools/definitions/query-region.tool.js CHANGED Viewed

@@ -29,16 +29,28 @@ const FeatureSchema = z.object({
         .array(z.string().describe('A clinical significance term for this variant.'))
         .optional()
         .describe('Clinical significance terms for variation features (e.g. pathogenic, benign).'),
+    parentId: z
+        .string()
+        .optional()
+        .describe('Parent transcript ID (ENST…) for exon features. An exon is reported once per parent ' +
+        'transcript it belongs to, so the same exon ID can appear on multiple rows that differ ' +
+        'only by this field — not duplicates.'),
+    rank: z
+        .number()
+        .optional()
+        .describe('Position (1-based) of an exon within its parent transcript.'),
 });
 export const ensemblQueryRegion = tool('ensembl_query_region', {
     title: 'Query Genomic Region',
     description: 'Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory ' +
         'elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name. ' +
         'Useful for "what\'s in this locus?" and for seeding follow-up lookups. Region format is chr:start-end ' +
-        '(e.g. 13:32315086-32400268 for the BRCA2 locus). Chromosome names use Ensembl format — no "chr" ' +
-        'prefix for vertebrates (use 13 not chr13). The feature parameter defaults to gene only to prevent ' +
-        'overwhelming returns — requesting variation in an 85 kb region returns 44,000+ entries. Explicitly ' +
-        'include variation, regulatory, transcript, or exon only when needed.',
+        '(e.g. 13:32315086-32400268 for the BRCA2 locus). Ensembl normalizes chromosome names and canonical ' +
+        'vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also ' +
+        'accepted. The feature parameter defaults to gene only to prevent overwhelming returns — requesting ' +
+        'variation in an 85 kb region returns 44,000+ entries. Explicitly include variation, regulatory, ' +
+        'transcript, or exon only when needed. Exon rows carry the parent transcript ID, so the same exon ' +
+        'appears once per transcript it belongs to.',
     annotations: { readOnlyHint: true, openWorldHint: true, idempotentHint: true },
     input: z.object({
         species: z
@@ -48,7 +60,8 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
         region: z
             .string()
             .describe('Genomic region in chr:start-end format (e.g. 13:32315086-32400268). ' +
-            'Chromosome names use Ensembl format — no "chr" prefix for vertebrates (13, not chr13). ' +
+            'Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix ' +
+            '(13, not chr13); a chr-prefixed name like chr13 is also accepted. ' +
             'For large regions (>100 kb), limit to gene feature type to avoid overwhelming results.'),
         feature: z
             .array(z
@@ -83,7 +96,8 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
             code: JsonRpcErrorCode.ValidationError,
             when: 'The region string could not be parsed or contains invalid coordinates.',
             recovery: 'Use the format chr:start-end (e.g. 13:32315086-32400268). ' +
-                'Chromosome names use Ensembl format with no "chr" prefix for vertebrates. ' +
+                'Chromosome names normalize either way — canonical vertebrate names omit the chr prefix ' +
+                '(13, not chr13), but a chr-prefixed name is also accepted. ' +
                 'Verify coordinates are within the chromosome bounds for the target assembly.',
         },
         {
@@ -117,8 +131,8 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
         });
         if (features.length === 0) {
             ctx.enrich.notice(`No ${input.feature.join(', ')} features found in ${input.region} for ${input.species}. ` +
-                'The region may be intergenic. Chromosome names use no "chr" prefix for vertebrates ' +
-                '(e.g. 13, not chr13). Use ensembl_lookup_gene to confirm locus coordinates.');
+                'The region may be intergenic, or the coordinates may not cover the intended locus. ' +
+                'Use ensembl_lookup_gene to confirm the locus coordinates.');
         }
         else if (features.length > 1000) {
             ctx.enrich.notice(`Large result set (${features.length} features). ` +
@@ -149,6 +163,9 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
             if (f.biotype)
                 lines.push(`**Biotype:** ${f.biotype}`);
             lines.push(`**Location:** ${f.chromosome}:${f.start}-${f.end}${f.strand != null ? ` strand:${f.strand} (${f.strand === -1 ? '-' : '+'})` : ''}`);
+            if (f.parentId) {
+                lines.push(`**Parent transcript:** ${f.parentId}${f.rank != null ? ` (exon rank ${f.rank})` : ''}`);
+            }
             if (f.description)
                 lines.push(`**Description:** ${f.description}`);
             if (f.consequenceType)

package/dist/mcp-server/tools/definitions/query-region.tool.js.map CHANGED Viewed

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

@@ -22,6 +22,7 @@ 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[]>;
+    predictVariantId(id: string, species: string, ctx: Context): Promise<VepRecord[]>;
     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[]>;

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

@@ -74,6 +74,11 @@ function normalizeOverlapFeature(raw) {
         ...(raw.clinical_significance?.length && {
             clinicalSignificance: raw.clinical_significance,
         }),
+        // Parent + rank are exon-specific here: an exon's Parent is its transcript.
+        // Other overlap types reuse `Parent` with different semantics (a transcript's
+        // Parent is its gene), so scope these to exons to avoid mislabeling other modes.
+        ...(raw.feature_type === 'exon' && raw.Parent && { parentId: raw.Parent }),
+        ...(raw.feature_type === 'exon' && typeof raw.rank === 'number' && { rank: raw.rank }),
     };
 }
 function normalizeVep(raw) {
@@ -322,6 +327,13 @@ export class EnsemblService {
             return [];
         return raw.map(normalizeVep);
     }
+    async predictVariantId(id, species, ctx) {
+        const path = `/vep/${encodeURIComponent(species)}/id/${encodeURIComponent(id)}`;
+        const raw = await this.fetchWithRetry(path, ctx);
+        if (!Array.isArray(raw))
+            return [];
+        return raw.map(normalizeVep);
+    }
     // --- Homology ---
     async getHomologyBySymbol(symbol, species, type, targetSpecies, ctx) {
         let path = `/homology/symbol/${encodeURIComponent(species)}/${encodeURIComponent(symbol)}?type=${encodeURIComponent(type)}`;

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

@@ -80,6 +80,10 @@ export type RawOverlapFeature = {
     clinical_significance?: string[];
     alleles?: string[];
     source?: string;
+    /** Parent transcript stable ID (ENST…) for exon overlap rows. */
+    Parent?: string;
+    /** 1-based position of an exon within its parent transcript. */
+    rank?: number;
 };
 export type RawVepTranscriptConsequence = {
     transcript_id?: string;
@@ -227,6 +231,14 @@ export type OverlapFeature = {
     description?: string;
     consequenceType?: string;
     clinicalSignificance?: string[];
+    /**
+     * Parent transcript stable ID (ENST…) for exon features. The same exon ID
+     * appears once per parent transcript it belongs to, so this is the
+     * discriminator that explains repeated exon rows in a region query.
+     */
+    parentId?: string;
+    /** 1-based rank of an exon within its parent transcript. */
+    rank?: number;
 };
 export type VepConsequence = {
     transcriptId?: string;

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

	@@ -1 +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": "0.3.0",
+  "version": "0.4.0",
   "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",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/ensembl-mcp-server",
     "source": "github"
   },
-  "version": "0.3.0",
+  "version": "0.4.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/ensembl-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.3.0",
+      "version": "0.4.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -55,7 +55,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/ensembl-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.3.0",
+      "version": "0.4.0",
       "packageArguments": [
         {
           "type": "positional",