npm - @cyanheads/protein-mcp-server - Versions diffs - 0.2.1 → 0.3.0 - Mend

@cyanheads/protein-mcp-server 0.2.1 → 0.3.0

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

Files changed (28) hide show

package/AGENTS.md +1 -1
package/CLAUDE.md +1 -1
package/README.md +21 -2
package/changelog/0.3.x/0.3.0.md +20 -0
package/dist/mcp-server/tools/definitions/_schemas.d.ts +10 -0
package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
package/dist/mcp-server/tools/definitions/_schemas.js +19 -0
package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts +22 -1
package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map +1 -1
package/dist/mcp-server/tools/definitions/get-annotations.tool.js +114 -4
package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map +1 -1
package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts +7 -0
package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
package/dist/mcp-server/tools/definitions/get-structure.tool.js +29 -1
package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
package/dist/services/rcsb/rcsb-service.d.ts +9 -3
package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
package/dist/services/rcsb/rcsb-service.js +24 -11
package/dist/services/rcsb/rcsb-service.js.map +1 -1
package/dist/services/rcsb/types.d.ts +9 -0
package/dist/services/rcsb/types.d.ts.map +1 -1
package/dist/services/shared/attribution.d.ts +42 -0
package/dist/services/shared/attribution.d.ts.map +1 -0
package/dist/services/shared/attribution.js +111 -0
package/dist/services/shared/attribution.js.map +1 -0
package/package.json +1 -1
package/server.json +3 -3

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.2.1
+**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

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.2.1
+**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

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.2.1-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/protein-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/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-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-v1.3.2-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/protein-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/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-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-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -62,6 +62,7 @@ Fetch structures with metadata and coordinate-file URLs, resolving across provid
 - `source: best_available` takes UniProt accessions and returns the top federated model (experimental if one exists, else the best prediction)
 - Per-ID partial success — unresolved IDs are listed in `failed[]`, not a batch-level error
 - `include_coords` inlines coordinate content; when a batch overflows the response budget it returns a per-structure size outline, so you can re-call with `sections: [ids]` for specific structures
+- Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))
 ---
@@ -119,8 +120,10 @@ Sequence and functional annotation for a protein.
 - UniProt features (domains, binding sites, PTMs) and natural sequence variants
 - InterPro domain/family memberships (Pfam, PROSITE, …) with associated GO terms
-- Provide a UniProt accession directly, or a PDB ID — resolved to its accession via the structure's sequence cross-reference
+- Provide a UniProt accession directly, or a PDB ID — resolved to a UniProt accession via the structure's sequence cross-reference
+- A multi-chain PDB entry can map to several accessions; the default is the deterministic lowest-author-chain pick, with the alternatives listed under `ambiguity`. Pass `chain` (an author chain ID, e.g. `A`) to select a specific one
 - `include` scopes which annotation classes are fetched: `features`, `domains`, `variants`, or `all`
+- Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))
 ## Resources
@@ -340,6 +343,22 @@ bun run devcheck
 bun run test
 ```
+## Upstream data licensing
+Structure and annotation data comes from public upstream databases, each under its own license. `protein_get_structure` and `protein_get_annotations` carry an `attribution` block on every response — the license, citation, and homepage for each source that contributed to that specific response — so the attribution obligation travels with the data to downstream consumers rather than living only here. CC BY / CC BY-SA sources require attribution on redistribution; CC0 sources are citation-only (attribution encouraged, not required).
+| Source | Contributes to | License |
+|:---|:---|:---|
+| [RCSB PDB](https://www.rcsb.org/) | `protein_get_structure` — experimental records | CC0 1.0 Universal |
+| [AlphaFold DB](https://alphafold.ebi.ac.uk/) | `protein_get_structure` — predicted models | CC BY 4.0 |
+| [SWISS-MODEL](https://swissmodel.expasy.org/) | `protein_get_structure` — `best_available` models | CC BY-SA 4.0 |
+| [BFVD](https://bfvd.steineggerlab.workers.dev/) | `protein_get_structure` — `best_available` models | CC BY 4.0 |
+| [UniProt](https://www.uniprot.org/) | `protein_get_annotations` | CC BY 4.0 |
+| [InterPro](https://www.ebi.ac.uk/interpro/) | `protein_get_annotations` — domain/family data | CC0 1.0 Universal |
+| [GO](https://geneontology.org/) | `protein_get_annotations` — GO terms | CC BY 4.0 |
+`best_available` federates predicted models through [3D-Beacons](https://3d-beacons.org/), so the `attribution` block credits the actual contributing provider (AlphaFold DB, SWISS-MODEL, BFVD, …); a provider without a curated license entry carries a `See provider terms` fallback pointing back to 3D-Beacons rather than a fabricated license. InterPro's own domain/family classifications are CC0; the GO terms carried alongside them are separately CC BY 4.0, so each is credited independently only when it actually contributes. Full citations for each source travel in the `attribution` block of the relevant tool responses. This covers upstream *data* licensing — the server's own code is licensed separately (see [License](#license)).
 ## License
 Apache-2.0 — see [LICENSE](LICENSE) for details.

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

@@ -0,0 +1,20 @@
+---
+summary: "protein_get_annotations disambiguates multi-chain PDB entries via a new chain input; protein_get_structure and protein_get_annotations both carry upstream data-source attribution (license + citation)."
+breaking: false
+security: false
+---
+# 0.3.0 — 2026-07-03
+## Added
+- **`protein_get_annotations` `chain`** — optional author chain ID (`auth_asym_id`) input disambiguates a multi-chain PDB entry to a specific UniProt accession; ignored when `uniprot` is supplied directly. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
+- **`protein_get_annotations` `ambiguity`** — new optional output field listing every distinct UniProt mapping (chains, accession, protein name) and a notice, present when a PDB ID resolves to more than one accession and no `chain` was given. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
+- **`chain_not_found`** — new declared error reason on `protein_get_annotations` for a supplied `chain` that matches no UniProt-mapped polymer entity in the resolved entry. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
+- **`attribution`** — new output field on `protein_get_structure` and `protein_get_annotations`: license, citation, and homepage for every upstream source that contributed to the response (RCSB PDB, AlphaFold DB, SWISS-MODEL, BFVD, UniProt, InterPro, GO). `best_available` credits the real federated 3D-Beacons provider; an uncurated provider gets an honest "See provider terms" fallback rather than a fabricated license. ([#7](https://github.com/cyanheads/protein-mcp-server/issues/7))
+- **README** — "Upstream data licensing" section documenting each source's license. ([#7](https://github.com/cyanheads/protein-mcp-server/issues/7))
+## Changed
+- **`RcsbService.resolveUniprot()`** → `resolveUniprotEntities()` — returns entity-grained `UniProtXref[]` (chains, accession, protein name) instead of a flat accession list. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
+- **`protein_get_annotations` unqualified PDB resolution** — now picks the deterministic lowest-author-chain accession instead of an order dependent on upstream GraphQL entity ordering. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))

package/dist/mcp-server/tools/definitions/_schemas.d.ts CHANGED Viewed

@@ -29,4 +29,14 @@ export type FacetDimensionOutput = z.infer<typeof facetDimensionSchema>;
 export declare function toFacetOutput(facet: FacetDimension, cap: number): FacetDimensionOutput;
 /** Render a list of facet dimensions to markdown lines for `format()` parity. */
 export declare function renderFacets(facets: FacetDimensionOutput[]): string[];
+/** License + citation for one upstream data source that contributed to a response. */
+export declare const attributionSchema: z.ZodObject<{
+    source: z.ZodString;
+    license: z.ZodString;
+    citation: z.ZodString;
+    homepage: z.ZodString;
+}, z.core.$strip>;
+export type AttributionOutput = z.infer<typeof attributionSchema>;
+/** Render an attribution list to one compact markdown line per source for `format()` parity. */
+export declare function renderAttribution(attributions: AttributionOutput[]): string[];
 //# sourceMappingURL=_schemas.d.ts.map

package/dist/mcp-server/tools/definitions/_schemas.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/_schemas.js CHANGED Viewed

@@ -84,4 +84,23 @@ export function renderFacets(facets) {
     }
     return lines;
 }
+/** License + citation for one upstream data source that contributed to a response. */
+export const attributionSchema = z
+    .object({
+    source: z
+        .string()
+        .describe('Contributing data-source display name (e.g. "RCSB PDB", "AlphaFold DB", "SWISS-MODEL", "UniProt"). Open-ended — best_available structures are federated through 3D-Beacons providers.'),
+    license: z.string().describe('License the source data is released under (e.g. "CC BY 4.0").'),
+    citation: z.string().describe('Primary-literature citation to credit the source.'),
+    homepage: z.string().describe('Source homepage (absolute URL).'),
+})
+    .describe('Upstream data-source attribution: license, citation, and homepage.');
+/** Render an attribution list to one compact markdown line per source for `format()` parity. */
+export function renderAttribution(attributions) {
+    const lines = [];
+    for (const a of attributions) {
+        lines.push(`- **${a.source}** (${a.license}) — ${a.citation} — ${a.homepage}`);
+    }
+    return lines;
+}
 //# sourceMappingURL=_schemas.js.map

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1	+ {"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,kCAAkC;AAClC,MAAM,gBAAgB,GAAG,CAAC;KACvB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;CAC/D,CAAC;KACD,QAAQ,CAAC,yDAAyD,CAAC,CAAC;AAEvE,kEAAkE;AAClE,MAAM,oBAAoB,GAAG,CAAC;KAC3B,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IACxD,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;IACvF,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,iFAAiF,CAAC;CAC/F,CAAC;KACD,QAAQ,CAAC,sDAAsD,CAAC,CAAC;AAEpE,kFAAkF;AAClF,MAAM,YAAY,GAAG,CAAC;KACnB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAC9D,QAAQ,EAAE,CAAC;SACR,KAAK,CAAC,oBAAoB,CAAC;SAC3B,QAAQ,EAAE;SACV,QAAQ,CACP,uFAAuF,CACxF;CACJ,CAAC;KACD,QAAQ,CAAC,gFAAgF,CAAC,CAAC;AAE9F,yCAAyC;AACzC,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC;KAClC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IAC3F,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,kEAAkE,CAAC;CAChF,CAAC;KACD,QAAQ,CAAC,gDAAgD,CAAC,CAAC;AAI9D,oFAAoF;AACpF,MAAM,UAAU,aAAa,CAAC,KAAqB,EAAE,GAAW;IAC9D,MAAM,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC;IAC7C,OAAO;QACL,SAAS,EAAE,KAAK,CAAC,SAAS;QAC1B,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC/C,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,GAAG,CAAC,CAAC,CAAC,QAAQ;gBACZ,CAAC,CAAC;oBACE,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;wBAC/B,SAAS,EAAE,CAAC,CAAC,SAAS;wBACtB,OAAO,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC;wBACpF,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;qBACvD,CAAC,CAAC;iBACJ;gBACH,CAAC,CAAC,EAAE,CAAC;SACR,CAAC,CAAC;QACH,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KAC1C,CAAC;AACJ,CAAC;AAED,iFAAiF;AACjF,MAAM,UAAU,YAAY,CAAC,MAA8B;IACzD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACvE,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YAC1B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACvC,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,QAAQ,IAAI,EAAE,EAAE,CAAC;gBACjC,MAAM,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,KAAK,KAAK,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBAC3E,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,MAAM,KAAK,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAClF,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,sFAAsF;AACtF,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,MAAM,CAAC;IACN,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,CACP,uLAAuL,CACxL;IACH,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+DAA+D,CAAC;IAC7F,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;IAClF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;CACjE,CAAC;KACD,QAAQ,CAAC,oEAAoE,CAAC,CAAC;AAIlF,gGAAgG;AAChG,MAAM,UAAU,iBAAiB,CAAC,YAAiC;IACjE,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,IAAI,YAAY,EAAE,CAAC;QAC7B,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,MAAM,OAAO,CAAC,CAAC,OAAO,OAAO,CAAC,CAAC,QAAQ,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;IACjF,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}

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

@@ -2,7 +2,8 @@
  * @fileoverview protein_get_annotations — sequence & functional annotation for a
  * protein: UniProt features (domains, binding sites, PTMs, variants) and InterPro
  * domain/family memberships with GO terms. Keyed by UniProt accession; resolves a
- * PDB ID to its accession when needed.
+ * PDB ID to its accession when needed — deterministically by default, by author
+ * chain when a multi-chain entry is ambiguous. Carries upstream data attribution.
  * @module mcp-server/tools/definitions/get-annotations.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -10,6 +11,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     uniprot: z.ZodOptional<z.ZodString>;
     pdb_id: z.ZodOptional<z.ZodString>;
+    chain: z.ZodOptional<z.ZodString>;
     include: z.ZodDefault<z.ZodEnum<{
         all: "all";
         features: "features";
@@ -46,11 +48,30 @@ export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefini
             category: z.ZodOptional<z.ZodString>;
         }, z.core.$strip>>;
     }, z.core.$strip>>>;
+    ambiguity: z.ZodOptional<z.ZodObject<{
+        accessions: z.ZodArray<z.ZodObject<{
+            chain: z.ZodArray<z.ZodString>;
+            accession: z.ZodString;
+            proteinName: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>;
+        notice: z.ZodString;
+    }, z.core.$strip>>;
+    attribution: z.ZodArray<z.ZodObject<{
+        source: z.ZodString;
+        license: z.ZodString;
+        citation: z.ZodString;
+        homepage: z.ZodString;
+    }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
     readonly reason: "no_uniprot_mapping";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.";
     readonly recovery: "Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.";
+}, {
+    readonly reason: "chain_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "A supplied chain matches no UniProt-mapped polymer entity in the resolved PDB entry.";
+    readonly recovery: "Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].chains in the pdb://{entry_id} resource).";
 }], {
     readonly resolvedFrom: z.ZodOptional<z.ZodString>;
     readonly notice: z.ZodOptional<z.ZodString>;

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwEjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6NzB,CAAC"}

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

@@ -2,14 +2,17 @@
  * @fileoverview protein_get_annotations — sequence & functional annotation for a
  * protein: UniProt features (domains, binding sites, PTMs, variants) and InterPro
  * domain/family memberships with GO terms. Keyed by UniProt accession; resolves a
- * PDB ID to its accession when needed.
+ * PDB ID to its accession when needed — deterministically by default, by author
+ * chain when a multi-chain entry is ambiguous. Carries upstream data attribution.
  * @module mcp-server/tools/definitions/get-annotations.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
+import { attributionsFor } from '../../../services/shared/attribution.js';
 import { isUniProtAccession } from '../../../services/shared/identifiers.js';
 import { getUniProtService } from '../../../services/uniprot/uniprot-service.js';
+import { attributionSchema, renderAttribution } from './_schemas.js';
 const featureSchema = z
     .object({
     type: z.string().describe('Feature type (e.g. Domain, Binding site, Modified residue).'),
@@ -40,12 +43,33 @@ const domainSchema = z
         .describe('Associated GO terms.'),
 })
     .describe('An InterPro domain/family membership with GO terms.');
+const ambiguitySchema = z
+    .object({
+    accessions: z
+        .array(z
+        .object({
+        chain: z
+            .array(z.string())
+            .describe('Author chain IDs (auth_asym_id) this entity covers (e.g. ["A", "C"]).'),
+        accession: z.string().describe('UniProt accession the chains map to.'),
+        proteinName: z.string().optional().describe('Polymer entity description.'),
+    })
+        .describe('One chain-group → UniProt accession mapping within the entry.'))
+        .describe('Every distinct UniProt mapping for the entry, lowest-chain first.'),
+    notice: z
+        .string()
+        .describe('Why multiple mappings exist and how to select one via the chain input.'),
+})
+    .describe('Present only when a PDB ID mapped to more than one distinct UniProt accession and no chain was supplied. The returned accession is the deterministic lowest-chain pick — re-call with chain set to a specific author chain ID to select another.');
 export const getAnnotations = tool('protein_get_annotations', {
     title: 'protein-mcp-server: get annotations',
     description: 'Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), ' +
         'natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a ' +
         "UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's " +
-        'sequence cross-reference. Use the "include" parameter to scope which annotation classes are fetched.',
+        'sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is ' +
+        'deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to ' +
+        'select a specific one. Use "include" to scope which annotation classes are fetched. Every response carries ' +
+        'an "attribution" block with the upstream data licenses and citations.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -54,6 +78,12 @@ export const getAnnotations = tool('protein_get_annotations', {
             when: 'A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.',
             recovery: 'Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.',
         },
+        {
+            reason: 'chain_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'A supplied chain matches no UniProt-mapped polymer entity in the resolved PDB entry.',
+            recovery: 'Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].chains in the pdb://{entry_id} resource).',
+        },
     ],
     input: z.object({
         uniprot: z
@@ -64,6 +94,10 @@ export const getAnnotations = tool('protein_get_annotations', {
             .string()
             .optional()
             .describe('PDB entry ID; resolved to a UniProt accession via cross-reference.'),
+        chain: z
+            .string()
+            .optional()
+            .describe('Author chain ID (auth_asym_id, e.g. "A") that disambiguates a multi-chain PDB entry to a specific UniProt accession. Case-sensitive — must match the author chain ID exactly (large structures can carry distinct "A" and "a" chains). Only applies with pdb_id; ignored when uniprot is supplied directly. See polymerEntities[].chains in the pdb://{entry_id} resource for an entry\'s author chain IDs.'),
         include: z
             .enum(['features', 'domains', 'variants', 'all'])
             .default('all')
@@ -79,6 +113,12 @@ export const getAnnotations = tool('protein_get_annotations', {
         features: z.array(featureSchema).optional().describe('Structural/functional features.'),
         variants: z.array(featureSchema).optional().describe('Natural sequence variants.'),
         domains: z.array(domainSchema).optional().describe('InterPro domain/family memberships.'),
+        ambiguity: ambiguitySchema
+            .optional()
+            .describe('Alternative UniProt mappings when a PDB ID resolved ambiguously (no chain given).'),
+        attribution: z
+            .array(attributionSchema)
+            .describe('Upstream data-source licenses and citations for every source that contributed to this response. Always present — the attribution obligation travels with the data.'),
     }),
     enrichment: {
         resolvedFrom: z
@@ -92,10 +132,37 @@ export const getAnnotations = tool('protein_get_annotations', {
         const rcsb = getRcsbService();
         let accession = input.uniprot?.toUpperCase();
         let resolvedFrom;
+        let ambiguity;
         if (!accession && input.pdb_id) {
-            const accessions = await rcsb.resolveUniprot(input.pdb_id, ctx);
-            accession = accessions[0];
+            const entities = await rcsb.resolveUniprotEntities(input.pdb_id, ctx);
             resolvedFrom = input.pdb_id.toUpperCase();
+            const chain = input.chain?.trim();
+            if (chain) {
+                const match = entities.find((e) => e.chains.includes(chain));
+                if (!match) {
+                    const available = entities.flatMap((e) => e.chains);
+                    throw ctx.fail('chain_not_found', `Chain "${chain}" matches no UniProt-mapped polymer entity in ${resolvedFrom}.`, {
+                        recovery: {
+                            hint: available.length
+                                ? `Author chains in ${resolvedFrom}: ${available.join(', ')}. Pass one of these, or omit chain for the deterministic default mapping.`
+                                : `${resolvedFrom} exposes no UniProt-mapped protein chains. Pass a UniProt accession directly.`,
+                        },
+                    });
+                }
+                accession = match.accession;
+            }
+            else {
+                // Deterministic default: order entities by their lowest author chain ID and
+                // take the first, so the same entry always yields the same accession
+                // regardless of upstream GraphQL entity ordering. When more than one distinct
+                // accession exists, surface the alternatives so the caller can pick a chain.
+                const ordered = orderByLowestChain(entities);
+                accession = ordered[0]?.accession;
+                const distinct = new Set(entities.map((e) => e.accession));
+                if (accession && distinct.size > 1) {
+                    ambiguity = buildAmbiguity(resolvedFrom, accession, ordered, distinct.size);
+                }
+            }
         }
         if (!accession) {
             throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.', { ...ctx.recoveryFor('no_uniprot_mapping') });
@@ -115,6 +182,15 @@ export const getAnnotations = tool('protein_get_annotations', {
         const variants = entry.features.filter((f) => f.category === 'variant');
         const wantFeatures = include === 'features' || include === 'all';
         const wantVariants = include === 'variants' || include === 'all';
+        // Attribution rides with the data. UniProt always contributes on success;
+        // InterPro only when it returned entries; GO only when a returned entry carries
+        // GO terms. InterPro (CC0) and GO (CC BY 4.0) are gated independently — an
+        // InterPro entry can exist with zero GO terms.
+        const sources = new Set(['UniProt']);
+        if (interpro.length > 0)
+            sources.add('InterPro');
+        if (interpro.some((d) => d.goTerms.length > 0))
+            sources.add('GO');
         if (resolvedFrom)
             ctx.enrich({ resolvedFrom });
         return {
@@ -127,6 +203,8 @@ export const getAnnotations = tool('protein_get_annotations', {
             ...(wantFeatures ? { features: toFeatureOutput(features) } : {}),
             ...(wantVariants ? { variants: toFeatureOutput(variants) } : {}),
             ...(wantInterPro ? { domains: interpro } : {}),
+            ...(ambiguity ? { ambiguity } : {}),
+            attribution: attributionsFor(sources),
         };
     },
     format: (result) => {
@@ -142,6 +220,13 @@ export const getAnnotations = tool('protein_get_annotations', {
             lines.push(head.join(' | '));
         if (result.function)
             lines.push(`\n**Function:** ${result.function}`);
+        if (result.ambiguity) {
+            lines.push(`\n### Multiple UniProt mappings`);
+            lines.push(result.ambiguity.notice);
+            for (const m of result.ambiguity.accessions) {
+                lines.push(`- **${m.accession}**${m.proteinName ? ` — ${m.proteinName}` : ''} (chains ${m.chain.join(', ') || 'none'})`);
+            }
+        }
         if (result.features && result.features.length > 0) {
             lines.push(`\n### Features (${result.features.length})`);
             for (const f of result.features)
@@ -160,9 +245,34 @@ export const getAnnotations = tool('protein_get_annotations', {
                     lines.push(`  - ${g.id} ${g.name}${g.category ? ` [${g.category}]` : ''}`);
             }
         }
+        if (result.attribution.length > 0) {
+            lines.push(`\n### Attribution`);
+            lines.push(...renderAttribution(result.attribution));
+        }
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });
+/** Lowest author chain ID for an entity (code-unit order); '' when it has none. */
+function lowestChain(entity) {
+    return [...entity.chains].sort()[0] ?? '';
+}
+/** Order UniProt xrefs by their lowest author chain ID — the deterministic default pick. */
+function orderByLowestChain(entities) {
+    return [...entities].sort((a, b) => lowestChain(a).localeCompare(lowestChain(b)));
+}
+/** Assemble the ambiguity block: every distinct mapping, lowest-chain first, with a notice. */
+function buildAmbiguity(entryId, chosen, ordered, distinctCount) {
+    return {
+        accessions: ordered.map((e) => ({
+            chain: e.chains,
+            accession: e.accession,
+            ...(e.proteinName ? { proteinName: e.proteinName } : {}),
+        })),
+        notice: `${entryId} maps to ${distinctCount} distinct UniProt accessions across its chains. ` +
+            `Returning ${chosen}, the deterministic lowest-chain pick. ` +
+            'Re-call with chain set to a specific author chain ID to select another.',
+    };
+}
 function toFeatureOutput(features) {
     return features.map((f) => ({
         type: f.type,

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

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

@@ -4,6 +4,7 @@
  * GraphQL call with per-ID partial success (`failed[]`). Optionally inlines
  * coordinate-file content; when that overflows a byte budget it returns a
  * per-structure section outline for targeted re-call instead of truncating.
+ * Carries upstream data attribution (RCSB PDB / AlphaFold DB) per response.
  * @module mcp-server/tools/definitions/get-structure.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -54,6 +55,12 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
         id: z.ZodString;
         reason: z.ZodString;
     }, z.core.$strip>>;
+    attribution: z.ZodArray<z.ZodObject<{
+        source: z.ZodString;
+        license: z.ZodString;
+        citation: z.ZodString;
+        homepage: z.ZodString;
+    }, z.core.$strip>>;
     overflow: z.ZodOptional<z.ZodObject<{
         sections: z.ZodArray<z.ZodObject<{
             id: z.ZodString;

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgEjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiQvB,CAAC"}

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

@@ -4,6 +4,7 @@
  * GraphQL call with per-ID partial success (`failed[]`). Optionally inlines
  * coordinate-file content; when that overflows a byte budget it returns a
  * per-structure section outline for targeted re-call instead of truncating.
+ * Carries upstream data attribution (RCSB PDB / AlphaFold DB) per response.
  * @module mcp-server/tools/definitions/get-structure.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -14,8 +15,10 @@ import { getAlphaFoldService } from '../../../services/alphafold/alphafold-servi
 import { getBeaconsService } from '../../../services/beacons/beacons-service.js';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
 import { mapWithConcurrency } from '../../../services/shared/async.js';
+import { attributionsFor } from '../../../services/shared/attribution.js';
 import { fetchText } from '../../../services/shared/http.js';
 import { isPdbId, isUniProtAccession } from '../../../services/shared/identifiers.js';
+import { attributionSchema, renderAttribution } from './_schemas.js';
 const confidenceBucketsSchema = z.object({
     veryLow: z.number().describe('Fraction of residues with pLDDT < 50.'),
     low: z.number().describe('Fraction with pLDDT 50–70.'),
@@ -115,6 +118,9 @@ export const getStructure = tool('protein_get_structure', {
         })
             .describe('A requested ID that did not resolve, with the reason.'))
             .describe('IDs that could not be resolved (partial success).'),
+        attribution: z
+            .array(attributionSchema)
+            .describe('Upstream data-source licenses and citations for every source present in structures[] — RCSB PDB for experimental records, AlphaFold DB for predicted. Always present — the attribution obligation travels with the data.'),
         overflow: z
             .object({
             sections: z
@@ -192,7 +198,25 @@ export const getStructure = tool('protein_get_structure', {
         if (failed.length > 0) {
             ctx.enrich.notice(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
         }
-        return { structures, failed, ...(overflow ? { overflow } : {}) };
+        // Attribution is a per-response union of the sources actually present, keyed
+        // off each record's real provider. Experimental data is fetched from RCSB
+        // regardless of the beacon's provider label. best_available federates predicted
+        // models through 3D-Beacons (AlphaFold DB, SWISS-MODEL, BFVD, …), so a predicted
+        // record's provider — not the binary source — determines the credit; an
+        // uncurated provider falls back to an honest no-license entry. Crediting every
+        // predicted model as AlphaFold would mis-attribute a SWISS-MODEL structure.
+        const sources = new Set();
+        for (const s of structures) {
+            sources.add(s.source === 'experimental'
+                ? 'RCSB PDB'
+                : (s.provider ?? '3D-Beacons (provider unspecified)'));
+        }
+        return {
+            structures,
+            failed,
+            attribution: attributionsFor(sources),
+            ...(overflow ? { overflow } : {}),
+        };
     },
     format: (result) => {
         const lines = [`## Structures (${result.structures.length})`];
@@ -239,6 +263,10 @@ export const getStructure = tool('protein_get_structure', {
             for (const s of result.overflow.sections)
                 lines.push(`- ${s.id}: ${s.bytes} bytes`);
         }
+        if (result.attribution.length > 0) {
+            lines.push(`\n### Attribution`);
+            lines.push(...renderAttribution(result.attribution));
+        }
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });

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

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

@@ -11,7 +11,7 @@ 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 { ServerConfig } from '../../config/server-config.js';
-import type { BindingSite, ChemComp, ContentType, EntryMeta, FacetDimension, SearchResult, StructureSearchParams } from './types.js';
+import type { BindingSite, ChemComp, ContentType, EntryMeta, FacetDimension, SearchResult, StructureSearchParams, UniProtXref } from './types.js';
 /** RCSB return types relevant to this server. */
 export type ReturnType = 'entry' | 'polymer_entity' | 'mol_definition';
 /** A facet dimension request: friendly name + how RCSB should aggregate it. */
@@ -56,8 +56,14 @@ export declare class RcsbService {
     }>;
     /** Batched entry metadata for up to N PDB IDs in one GraphQL call. */
     getEntries(ids: string[], ctx: Context): Promise<EntryMeta[]>;
-    /** Resolve a PDB entry to its cross-referenced UniProt accession(s). */
-    resolveUniprot(pdbId: string, ctx: Context): Promise<string[]>;
+    /**
+     * Resolve a PDB entry to its UniProt-cross-referenced polymer entities. Each
+     * returned entry carries the author chain IDs it covers, the mapped UniProt
+     * accession, and the polymer description — entity-grained so a caller can
+     * disambiguate a multi-chain entry by chain. One entry per polymer entity that
+     * carries a UniProt xref; entities without one are skipped. Single round trip.
+     */
+    resolveUniprotEntities(pdbId: string, ctx: Context): Promise<UniProtXref[]>;
     /** First polymer entity's one-letter sequence for a PDB entry. */
     getSequence(pdbId: string, ctx: Context): Promise<{
         entityId: string;

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

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

@@ -137,19 +137,30 @@ export class RcsbService {
         const data = await this.graphql(ENTRIES_QUERY, { ids: ids.map((id) => id.toUpperCase()) }, ctx, 'RcsbService.getEntries');
         return (data.entries ?? []).filter((e) => e != null).map(normalizeEntry);
     }
-    /** Resolve a PDB entry to its cross-referenced UniProt accession(s). */
-    async resolveUniprot(pdbId, ctx) {
-        const data = await this.graphql(XREF_QUERY, { id: pdbId.toUpperCase() }, ctx, 'RcsbService.resolveUniprot');
-        const accessions = new Set();
+    /**
+     * Resolve a PDB entry to its UniProt-cross-referenced polymer entities. Each
+     * returned entry carries the author chain IDs it covers, the mapped UniProt
+     * accession, and the polymer description — entity-grained so a caller can
+     * disambiguate a multi-chain entry by chain. One entry per polymer entity that
+     * carries a UniProt xref; entities without one are skipped. Single round trip.
+     */
+    async resolveUniprotEntities(pdbId, ctx) {
+        const data = await this.graphql(XREF_QUERY, { id: pdbId.toUpperCase() }, ctx, 'RcsbService.resolveUniprotEntities');
+        const xrefs = [];
         for (const entity of data.entry?.polymer_entities ?? []) {
-            for (const ref of entity.rcsb_polymer_entity_container_identifiers
-                ?.reference_sequence_identifiers ?? []) {
-                if (/uniprot/i.test(ref.database_name ?? '') && ref.database_accession) {
-                    accessions.add(ref.database_accession.toUpperCase());
-                }
-            }
+            const container = entity.rcsb_polymer_entity_container_identifiers;
+            const accession = container?.reference_sequence_identifiers?.find((ref) => /uniprot/i.test(ref.database_name ?? '') && ref.database_accession)?.database_accession;
+            if (!accession)
+                continue;
+            xrefs.push({
+                accession: accession.toUpperCase(),
+                chains: container?.auth_asym_ids ?? [],
+                ...(entity.rcsb_polymer_entity?.pdbx_description
+                    ? { proteinName: entity.rcsb_polymer_entity.pdbx_description }
+                    : {}),
+            });
         }
-        return [...accessions];
+        return xrefs;
     }
     /** First polymer entity's one-letter sequence for a PDB entry. */
     async getSequence(pdbId, ctx) {
@@ -439,7 +450,9 @@ const ENTRIES_QUERY = `query Entries($ids: [String!]!) {
 const XREF_QUERY = `query Xref($id: String!) {
   entry(entry_id: $id) {
     polymer_entities {
+      rcsb_polymer_entity { pdbx_description }
       rcsb_polymer_entity_container_identifiers {
+        auth_asym_ids
         reference_sequence_identifiers { database_accession database_name }
       }
     }

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

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

@@ -55,6 +55,15 @@ export interface PolymerEntityMeta {
     /** Residue count of the sample sequence. */
     sequenceLength?: number;
 }
+/** One polymer entity's UniProt cross-reference: the chains it covers and the mapped accession. */
+export interface UniProtXref {
+    /** UniProt accession this entity maps to. */
+    accession: string;
+    /** Author chain IDs (auth_asym_id) this entity covers (e.g. ["A", "C"]). */
+    chains: string[];
+    /** Polymer entity description (e.g. "Hemoglobin subunit alpha"). */
+    proteinName?: string;
+}
 /** A bound non-polymer (ligand) component within an entry. */
 export interface LigandMeta {
     /** Chemical component ID (e.g. `HEM`, `STI`). */

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

	@@ -1 +1 @@
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package/dist/services/shared/attribution.d.ts ADDED Viewed

@@ -0,0 +1,42 @@
+/**
+ * @fileoverview Upstream data-source attribution — the license and citation each
+ * contributing database asks to travel with its data. `protein_get_structure` and
+ * `protein_get_annotations` project the sources that actually contributed to a
+ * response into a deduped attribution array, so the obligation rides with the data
+ * to every downstream consumer rather than living only in repo docs. Curated
+ * strings are verified against each source's primary license/citation page.
+ * `best_available` structures are federated through 3D-Beacons, an open set of
+ * model providers (AlphaFold DB, SWISS-MODEL, BFVD, AlphaFill, …), so an uncurated
+ * provider gets an honest fallback entry that asserts no license rather than a
+ * fabricated one. Pure data + a projection helper; the Zod output schema and
+ * renderer live in the tools' shared `_schemas.ts`.
+ * @module services/shared/attribution
+ */
+/**
+ * Curated data-source display names (verified license + citation), in canonical
+ * render order. The structure sources come first (RCSB PDB, then the federated
+ * predicted providers), followed by the annotation trio.
+ */
+export declare const CURATED_SOURCES: readonly ["RCSB PDB", "AlphaFold DB", "SWISS-MODEL", "BFVD", "UniProt", "InterPro", "GO"];
+/** A curated data-source display name with a verified license + citation. */
+export type CuratedSource = (typeof CURATED_SOURCES)[number];
+/** License, citation, and homepage for one contributing data source. */
+export interface Attribution {
+    /** Primary-literature citation the source asks consumers to cite. */
+    citation: string;
+    /** Source homepage. */
+    homepage: string;
+    /** License the source's data is released under (e.g. "CC BY 4.0"). */
+    license: string;
+    /** Data-source display name (a curated name, or a federated provider string). */
+    source: string;
+}
+/**
+ * Project the source names that contributed to a response into a deduped
+ * attribution array. Curated names render first in {@link CURATED_SOURCES} order;
+ * any uncurated provider follows, alphabetized, each with an honest fallback entry.
+ * The ordering is caller-insertion-independent, so an identical contributing set
+ * always renders identically.
+ */
+export declare function attributionsFor(sources: Iterable<string>): Attribution[];
+//# sourceMappingURL=attribution.d.ts.map

package/dist/services/shared/attribution.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/services/shared/attribution.js ADDED Viewed

@@ -0,0 +1,111 @@
+/**
+ * @fileoverview Upstream data-source attribution — the license and citation each
+ * contributing database asks to travel with its data. `protein_get_structure` and
+ * `protein_get_annotations` project the sources that actually contributed to a
+ * response into a deduped attribution array, so the obligation rides with the data
+ * to every downstream consumer rather than living only in repo docs. Curated
+ * strings are verified against each source's primary license/citation page.
+ * `best_available` structures are federated through 3D-Beacons, an open set of
+ * model providers (AlphaFold DB, SWISS-MODEL, BFVD, AlphaFill, …), so an uncurated
+ * provider gets an honest fallback entry that asserts no license rather than a
+ * fabricated one. Pure data + a projection helper; the Zod output schema and
+ * renderer live in the tools' shared `_schemas.ts`.
+ * @module services/shared/attribution
+ */
+/**
+ * Curated data-source display names (verified license + citation), in canonical
+ * render order. The structure sources come first (RCSB PDB, then the federated
+ * predicted providers), followed by the annotation trio.
+ */
+export const CURATED_SOURCES = [
+    'RCSB PDB',
+    'AlphaFold DB',
+    'SWISS-MODEL',
+    'BFVD',
+    'UniProt',
+    'InterPro',
+    'GO',
+];
+/**
+ * Canonical license + citation strings, keyed by source. Verified against each
+ * source's primary license/citation page. CC BY / CC BY-SA sources require
+ * attribution to travel with redistributed data; CC0 sources are citation-only
+ * (attribution encouraged, not required) but carried here so the obligation is
+ * legible either way. InterPro's own domain/family data is CC0 — the CC BY 4.0 GO
+ * terms carried alongside it are a separate, independently-gated source.
+ */
+const ATTRIBUTIONS = {
+    'RCSB PDB': {
+        source: 'RCSB PDB',
+        license: 'CC0 1.0 Universal',
+        citation: 'H.M. Berman et al., "The Protein Data Bank," Nucleic Acids Research 28:235–242 (2000). DOI: 10.1093/nar/28.1.235',
+        homepage: 'https://www.rcsb.org/',
+    },
+    'AlphaFold DB': {
+        source: 'AlphaFold DB',
+        license: 'CC BY 4.0',
+        citation: 'Jumper et al., "Highly accurate protein structure prediction with AlphaFold," Nature 596:583–589 (2021). DOI: 10.1038/s41586-021-03819-2; Bertoni et al., "AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage," Nucleic Acids Research 54(D1):D358–D362 (2025). DOI: 10.1093/nar/gkaf1226',
+        homepage: 'https://alphafold.ebi.ac.uk/',
+    },
+    'SWISS-MODEL': {
+        source: 'SWISS-MODEL',
+        license: 'CC BY-SA 4.0',
+        citation: 'Waterhouse et al., "SWISS-MODEL: homology modelling of protein structures and complexes," Nucleic Acids Research 46(W1):W296–W303 (2018). DOI: 10.1093/nar/gky427; Bienert et al., "The SWISS-MODEL Repository—new features and functionality," Nucleic Acids Research 45(D1):D313–D319 (2017). DOI: 10.1093/nar/gkw1132',
+        homepage: 'https://swissmodel.expasy.org/',
+    },
+    BFVD: {
+        source: 'BFVD',
+        license: 'CC BY 4.0',
+        citation: 'Kim et al., "BFVD—a large repository of predicted viral protein structures," Nucleic Acids Research 53(D1):D340–D347 (2025). DOI: 10.1093/nar/gkae1119',
+        homepage: 'https://bfvd.steineggerlab.workers.dev/',
+    },
+    UniProt: {
+        source: 'UniProt',
+        license: 'CC BY 4.0',
+        citation: 'The UniProt Consortium, "UniProt: the Universal Protein Knowledgebase in 2025," Nucleic Acids Research 53(D1):D609–D617 (2025). DOI: 10.1093/nar/gkae1010',
+        homepage: 'https://www.uniprot.org/',
+    },
+    InterPro: {
+        source: 'InterPro',
+        license: 'CC0 1.0 Universal',
+        citation: 'Blum et al., "InterPro: the protein sequence classification resource in 2025," Nucleic Acids Research 53(D1):D444–D456 (2025). DOI: 10.1093/nar/gkae1082',
+        homepage: 'https://www.ebi.ac.uk/interpro/',
+    },
+    GO: {
+        source: 'GO',
+        license: 'CC BY 4.0',
+        citation: 'Ashburner et al., "Gene Ontology: tool for the unification of biology," Nature Genetics 25:25–29 (2000). DOI: 10.1038/75556; Gene Ontology Consortium, "The Gene Ontology knowledgebase in 2026," Nucleic Acids Research 54(D1):D1779–D1792 (2026). DOI: 10.1093/nar/gkaf1292',
+        homepage: 'https://geneontology.org/',
+    },
+};
+const CURATED_NAMES = new Set(CURATED_SOURCES);
+/**
+ * Honest fallback for an uncurated federated provider (AlphaFill, or any 3D-Beacons
+ * provider without a verified license entry). Asserts no license — better to point
+ * the consumer at the provider's own terms than to fabricate one.
+ */
+function fallbackAttribution(source) {
+    return {
+        source,
+        license: 'See provider terms',
+        citation: 'Federated via 3D-Beacons — consult the provider for citation and license terms.',
+        homepage: 'https://3d-beacons.org/',
+    };
+}
+/**
+ * Project the source names that contributed to a response into a deduped
+ * attribution array. Curated names render first in {@link CURATED_SOURCES} order;
+ * any uncurated provider follows, alphabetized, each with an honest fallback entry.
+ * The ordering is caller-insertion-independent, so an identical contributing set
+ * always renders identically.
+ */
+export function attributionsFor(sources) {
+    const wanted = new Set(sources);
+    const curated = CURATED_SOURCES.filter((s) => wanted.has(s)).map((s) => ATTRIBUTIONS[s]);
+    const uncurated = [...wanted]
+        .filter((s) => !CURATED_NAMES.has(s))
+        .sort()
+        .map(fallbackAttribution);
+    return [...curated, ...uncurated];
+}
+//# sourceMappingURL=attribution.js.map

package/dist/services/shared/attribution.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.2.1",
+  "version": "0.3.0",
   "mcpName": "io.github.cyanheads/protein-mcp-server",
   "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.2.1",
+  "version": "0.3.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.2.1",
+      "version": "0.3.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.2.1",
+      "version": "0.3.0",
       "packageArguments": [
         {
           "type": "positional",