@pipeworx/mcp-pombase 0.1.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2026 Pipeworx
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# mcp-pombase
+
+PomBase MCP — the fission yeast (Schizosaccharomyces pombe) model-organism database.
+
+Part of [Pipeworx](https://pipeworx.io) — an MCP gateway connecting AI agents to 823+ live data sources.
+
+## Tools
+
+| Tool | Description |
+|------|-------------|
+
+## Quick Start
+
+Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
+
+```json
+{
+  "mcpServers": {
+    "pombase": {
+      "url": "https://gateway.pipeworx.io/pombase/mcp"
+    }
+  }
+}
+```
+
+Or connect to the full Pipeworx gateway for access to all 823+ data sources:
+
+```json
+{
+  "mcpServers": {
+    "pipeworx": {
+      "url": "https://gateway.pipeworx.io/mcp"
+    }
+  }
+}
+```
+
+## Using with ask_pipeworx
+
+Instead of calling tools directly, you can ask questions in plain English:
+
+```
+ask_pipeworx({ question: "your question about Pombase data" })
+```
+
+The gateway picks the right tool and fills the arguments automatically.
+
+## More
+
+- [All tools and guides](https://github.com/pipeworx-io/examples)
+- [pipeworx.io](https://pipeworx.io)
+
+## License
+
+MIT

package/package.json

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+{
+  "name": "@pipeworx/mcp-pombase",
+  "version": "0.1.0",
+  "description": "PomBase MCP — the fission yeast (Schizosaccharomyces pombe) model-organism database.",
+  "type": "module",
+  "main": "src/index.ts",
+  "types": "src/index.ts",
+  "keywords": ["mcp", "mcp-server", "model-context-protocol", "pipeworx", "pombase"],
+  "license": "MIT",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/pipeworx-io/mcp-pombase"
+  },
+  "scripts": {
+    "typecheck": "tsc --noEmit"
+  },
+  "devDependencies": {
+    "typescript": "^5.7.0"
+  }
+}

package/server.json

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+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.pipeworx-io/pombase",
+  "title": "Pombase",
+  "description": "PomBase MCP — the fission yeast (Schizosaccharomyces pombe) model-organism database.",
+  "version": "0.1.0",
+  "websiteUrl": "https://pipeworx.io/packs/pombase",
+  "repository": {
+    "url": "https://github.com/pipeworx-io/mcp-pombase",
+    "source": "github"
+  },
+  "remotes": [
+    {
+      "type": "streamable-http",
+      "url": "https://gateway.pipeworx.io/pombase/mcp"
+    }
+  ]
+}

package/src/index.ts

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+interface McpToolDefinition {
+  name: string;
+  description: string;
+  inputSchema: {
+    type: 'object';
+    properties: Record<string, unknown>;
+    required?: string[];
+  };
+}
+
+interface McpToolExport {
+  tools: McpToolDefinition[];
+  callTool: (name: string, args: Record<string, unknown>) => Promise<unknown>;
+  meter?: { credits: number };
+  cost?: Record<string, unknown>;
+  provider?: string;
+}
+
+/**
+ * PomBase MCP — the fission yeast (Schizosaccharomyces pombe) model-organism database.
+ *
+ * Keyless JSON API. Look up a gene by its PomBase systematic id and get its
+ * product, protein domains (InterPro), deletion viability, UniProt id, and
+ * curation status; or look up a curated publication by PubMed id.
+ * Complements SGD (budding yeast).
+ *
+ * Base: https://www.pombase.org/api/v1/dataset/latest
+ */
+
+
+const BASE = 'https://www.pombase.org/api/v1/dataset/latest';
+const UA = 'pipeworx/1.0 (+https://pipeworx.io)';
+
+const tools: McpToolExport['tools'] = [
+  {
+    name: 'get_gene',
+    description:
+      'PomBase (fission yeast / S. pombe model-organism DB): look up a gene by its PomBase systematic id and return its product, protein domains (InterPro), deletion viability, UniProt id, and curation status. Keyless. NOTE: requires a systematic id like "SPAC1002.01" or "SPBC2F12.13" — standard gene names like "cdc2" are NOT resolved by this API. Complements SGD (budding yeast).',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        id: {
+          type: 'string',
+          description: 'A PomBase systematic id, e.g. "SPAC1002.01" or "SPBC2F12.13". Standard names ("cdc2") are not accepted.',
+        },
+      },
+      required: ['id'],
+    },
+  },
+  {
+    name: 'get_reference',
+    description:
+      'PomBase: look up a curated S. pombe publication by its PubMed id (e.g. "PMID:11739790") and return its title, citation, authors, year, abstract, and how many genes it annotates. Keyless.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        pmid: {
+          type: 'string',
+          description: 'A PubMed id, with or without the "PMID:" prefix, e.g. "PMID:11739790" or "11739790".',
+        },
+      },
+      required: ['pmid'],
+    },
+  },
+];
+
+interface InterProMatch {
+  interpro_id?: string;
+  interpro_description?: string;
+  id?: string;
+  description?: string;
+}
+
+async function callTool(name: string, args: Record<string, unknown>): Promise<unknown> {
+  try {
+    switch (name) {
+      case 'get_gene':
+        return await getGene(args);
+      case 'get_reference':
+        return await getReference(args);
+      default:
+        return { error: `Unknown tool: ${name}` };
+    }
+  } catch (err) {
+    return { error: err instanceof Error ? err.message : String(err) };
+  }
+}
+
+async function getGene(args: Record<string, unknown>): Promise<unknown> {
+  const id = reqStr(args, 'id');
+  const res = await pombaseGet(`/data/gene/${encodeURIComponent(id)}`);
+  if (res.status === 404 || res.status === 410) return { error: 'gene not found', id };
+  if (!res.ok) return { error: `PomBase: ${res.status} ${(await res.text()).slice(0, 200)}` };
+
+  const gene = (await res.json()) as Record<string, unknown> | null;
+  if (!gene || typeof gene !== 'object') return { error: 'gene not found', id };
+
+  const matches = Array.isArray(gene.interpro_matches) ? (gene.interpro_matches as InterProMatch[]) : [];
+  const tmCoords = Array.isArray(gene.tm_domain_coords) ? gene.tm_domain_coords : [];
+
+  return {
+    systematic_id: gene.uniquename ?? null,
+    name: gene.name ?? null,
+    product: gene.product ?? null,
+    taxonid: gene.taxonid ?? null,
+    feature_type: gene.feature_type ?? null,
+    characterisation_status: gene.characterisation_status ?? null,
+    deletion_viability: gene.deletion_viability ?? null,
+    uniprot: gene.uniprot_identifier ?? null,
+    interpro: matches.map((m) => ({
+      id: m.interpro_id ?? m.id ?? null,
+      description: m.interpro_description ?? m.description ?? null,
+    })),
+    tm_domains: tmCoords.length,
+  };
+}
+
+async function getReference(args: Record<string, unknown>): Promise<unknown> {
+  let pmid = reqStr(args, 'pmid').trim();
+  if (!/^PMID:/i.test(pmid)) pmid = `PMID:${pmid.replace(/^PMID:?/i, '')}`;
+
+  const res = await pombaseGet(`/data/reference/${encodeURIComponent(pmid)}`);
+  if (res.status === 404 || res.status === 410) return { error: 'reference not found', pmid };
+  if (!res.ok) return { error: `PomBase: ${res.status} ${(await res.text()).slice(0, 200)}` };
+
+  const ref = (await res.json()) as Record<string, unknown> | null;
+  if (!ref || typeof ref !== 'object') return { error: 'reference not found', pmid };
+
+  return {
+    pmid: ref.uniquename ?? pmid,
+    title: ref.title ?? null,
+    citation: ref.citation ?? null,
+    authors: ref.authors ?? null,
+    authors_abbrev: ref.authors_abbrev ?? null,
+    publication_year: ref.publication_year ?? null,
+    abstract: ref.abstract ?? null,
+    curated_gene_count: ref.gene_count ?? null,
+  };
+}
+
+async function pombaseGet(path: string): Promise<Response> {
+  return fetch(`${BASE}${path}`, {
+    headers: { Accept: 'application/json', 'User-Agent': UA },
+  });
+}
+
+function reqStr(args: Record<string, unknown>, key: string): string {
+  const v = args[key];
+  if (typeof v !== 'string' || !v.trim()) {
+    throw new Error(`Required argument "${key}" is missing.`);
+  }
+  return v;
+}
+
+export default { tools, callTool, meter: { credits: 1 } } satisfies McpToolExport;

package/tsconfig.json

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+{
+  "compilerOptions": {
+    "target": "ES2022",
+    "module": "ESNext",
+    "moduleResolution": "bundler",
+    "strict": true,
+    "esModuleInterop": true,
+    "skipLibCheck": true,
+    "outDir": "dist",
+    "rootDir": "src",
+    "declaration": true
+  },
+  "include": ["src"]
+}