cellosaurus-mcp-server

MCP server for the SIB Cellosaurus API — the reference knowledge resource on cell lines (~169,000 cell lines: cancer lines, hybridomas, iPSC/ESC, patient-derived, etc.), each keyed by a stable CVCL_ accession and cross-referenced to ~100 other databases (CCLE/DepMap, Cosmic, ATCC, ChEMBL, PubMed, NCBI Taxonomy, NCIt disease, …).

• Upstream API: https://api.cellosaurus.org (OpenAPI: https://api.cellosaurus.org/openapi.json)
• Upstream site / docs: https://www.cellosaurus.org
• Auth: none
• License: CC BY 4.0 (surfaced as verifiable _meta.citation on every cellosaurus_execute result)
• Response format: JSON by default (adapter sends Accept: application/json); format=xml|txt|tsv returned as { text }
• Release at build time: v56.0 (~168,970 cell lines)

Endpoints (curated from the upstream OpenAPI)

Only three GET methods exist upstream; all are curated in src/spec/catalog.ts:

• GET /cell-line/{ac} — fetch one record by CVCL accession (category cell-line)
• GET /search/cell-line — Solr search (q=, start, rows, fields, sort) (category search)
• GET /release-info — dataset version / counts (category release)

REST only. Cellosaurus also serves SPARQL/RDF (https://sparql.cellosaurus.org) — noted as a future option, not wired here.

Tools (Code Mode only)

• cellosaurus_search — discover the 3 curated endpoints + usage notes from the catalog
• cellosaurus_execute — run sandboxed JavaScript against the API via api.get() (carries _meta.citation)
• cellosaurus_query_data — SQL over staged responses
• cellosaurus_get_schema — inspect staged-dataset schemas

Large, well-annotated records (e.g. HeLa CVCL_0030 ≈ 450 KB, Caco-2 CVCL_0025 ≈ 130 KB compact JSON — verified live) auto-stage past the 30 KB inline threshold into CellosaurusDataDO; child arrays (comment-list, xref-list, reference-list, sequence-variation-list, …) become SQLite tables. Trim payloads with fields= (or a small rows=) to keep responses inline.

Example (Code Mode)

// Resolve HeLa and list its cross-references (dr = xref-list)
const resp = await api.get('/cell-line/{ac}', { ac: 'CVCL_0030', fields: 'id,ac,ox,di,dr' });
const cl = resp.Cellosaurus['cell-line-list'][0];
return {
  name: cl['name-list'].find(n => n.type === 'identifier')?.value,
  accession: cl['accession-list'].find(a => a.type === 'primary')?.value,
  xrefs: (cl['xref-list'] || []).map(x => `${x.database}:${x.accession}`),
};

// Find human cell lines that have a Cosmic-CLP cross-reference
const resp = await api.get('/search/cell-line', {
  q: 'ox:9606 AND dr:Cosmic-CLP', rows: 20, fields: 'id,ac,di',
});
return resp.Cellosaurus['cell-line-list'].map(c => c['accession-list'][0].value);