API & MCP

What's available

REST base URL

https://affinage-plasmodium.wi.mit.edu/api

MCP endpoint

https://affinage-plasmodium.wi.mit.edu/mcp

Interactive REST docs

/docs (Swagger UI)

REST endpoints

The site holds 6,740 gene cards, of which 2,485 carry a literature-derived annotation (at least one reading-pass discovery). The other 4,255 have no discoveries and no teleology; 4,255 of them return the placeholder narrative “No mechanistic discoveries found in literature.” — but a corpus may still be present: 1,221 of those cards have citation-ranked papers under /api/corpus, so check the corpus before concluding Affinage has nothing on a gene. The placeholder means Affinage found no mechanistic findings for the gene — it is not a finding that the gene is uncharacterised.

A further 3 annotated cards carry a refusal narrative that begins “Insufficient on-target evidence to synthesize a narrative.”: the reading pass found papers, but the synthesis pass judged none of them to be about the queried gene. Their discoveries are still served. Treat the exact placeholder, or a narrative beginning “Insufficient on-target evidence”, as a no-data result; a few annotated cards have narratives beginning “No mechanistic findings specific to…” that still carry discoveries, so check /api/discoveries before discarding a card. Live row counts: /healthz.

MCP tools

Ten read-only tools mirror the REST endpoints above. They accept typed arguments (gene name or ID, PMID, row limit) and return structured JSON. The same coverage caveats apply.

• get_gene
• get_mechanistic_narrative
• get_discoveries
• get_teleology
• get_mechanism_profile
• get_uniprot
• get_audit_flag
• get_corpus
• get_paper
• search_genes

Lookups resolve a gene name, any species' PlasmoDB gene ID, or an alias to the same card: AMA1, PF3D7_1133400 (Pf), PBANKA_0915000 (Pb) and PKNH_0931500 (Pk) all reach the AMA1 card, and the response carries resolved_from so you can see the redirect. Cards are keyed by the Pf ID where the card has one, otherwise by the Pb or Pk ID. Where a name is shared by several cards the lookup resolves only when one card stands out (most specific kind, then annotated, then P. falciparum); a product description carried by many cards is not resolved. /api/search?q= lists every card carrying an exact name or ID match first, in that order, then narrative text — use it when a name is not found. If a name does not resolve, look the ID up in PlasmoDB rather than concluding the gene is absent.

This server covers Plasmodium only. Gene nicknames collide across organisms, so a name that also exists in human or Toxoplasma will never return that organism's gene. Findings are attributed to the specific species the work was done in — do not carry a result from P. falciparum over to P. berghei. GET /api/gene/{symbol} and get_gene return the card's member gene per species as strains (species code, gene_id, name, product, UniProt accession); discoveries carry no species column, so per-finding attribution lives in the narrative text.

Recipes

Click a surface to expand its recipe. Each one is a complete setup — no other steps needed unless noted.

# curl
curl https://affinage-plasmodium.wi.mit.edu/api/mechanistic_narrative/PF3D7_1133400

# Python
import requests
r = requests.get("https://affinage-plasmodium.wi.mit.edu/api/mechanistic_narrative/PF3D7_1133400")
print(r.json()["mechanistic_narrative"])

https://affinage-plasmodium.wi.mit.edu/mcp

{
  "mcpServers": {
    "affinage-plasmodium": {
      "command": "npx",
      "args": ["-y", "mcp-remote", "https://affinage-plasmodium.wi.mit.edu/mcp"]
    }
  }
}

claude mcp add affinage-plasmodium --transport http https://affinage-plasmodium.wi.mit.edu/mcp

{
  "mcpServers": {
    "affinage-plasmodium": {
      "url": "https://affinage-plasmodium.wi.mit.edu/mcp"
    }
  }
}