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Deterministic, verifiable data for agents.

One hosted MCP server and one CLI over the primary biological databases — the same correct result every run, with a manifest you can re-run and verify(). No portal to scrape.

Many record cards resolved into one verifiable manifest
$ claude mcp add --transport http pinakes https://mcp.pinakes.sh/mcp

Public reads need no key — add your pk_live_ key for an account. Any MCP client, the full config, and pinakes mcp install are in the docs.

Start free Read the docs →

Deterministic

Same query, same bytes, every run — snapshot-pinned and provable with a manifest.

Complete

Full retrieval, or it fails loudly. Never a silent truncation — the bug that put one outbreak’s origin anywhere from 1922 to 2014.

Agent-native

A typed MCP tool, not a website to click through.

See it run

Prefer the shell? Install the CLI, then watch determinism end to end — retrieve records, then verify the manifest reproduces them byte-for-byte.

$ curl -fsSL https://pinakes.sh/install | sh $ pinakes export --source-id ncbi-virus --filters 'organism:eq:Zaire ebolavirus' --snapshot-version 2026-06 106 records · complete · served_from snapshot@v7 · manifest written $ pinakes verify --manifest @manifest.json reproduced 106/106 · hash match · reproducible: true

Also pip install pinakes · brew install pinakes · conda. The command is always pinakes. Pre-launch: mcp.pinakes.sh, the packages, and the installer publish at launch — the commands above are the real, final shapes. See GitHub for current availability.

Biological databases for AI agents

Biology’s primary databases — plus arXiv literature — each served the same way, snapshot-pinned and provable with verify(). Ten ship in the first wave; 64 in all.

Ensembl
Genomics & sequence
Vertebrate genome annotation: genes, transcripts, regulation, comparative genomics, variation.First wave
UniProt
Proteins & families
Universal protein sequence and functional annotation knowledgebase (Swiss-Prot/TrEMBL).First waveCC-BY
PDB
Structure
Worldwide Protein Data Bank: experimentally determined 3D macromolecular structures.First waveCC0
AlphaFold DB
Structure
DeepMind/EMBL-EBI predicted protein structures across whole proteomes.First waveCC-BY
NCBI E-utilities
Genomics & sequence
Entrez programmatic access to GenBank, Gene, PubMed and dozens of NCBI databases.First waveindex/proxy
arXiv
Literature
Open-access preprint archive across physics, math, CS and quantitative biology.Stage 6
See the full catalog →

A preview of the intended catalog surface — connectors are in active development, not a live count.

Get a key

Free while Pinakes is in preview — the full catalog, reproducible retrieval, and verify(), all at the base rate limits. No tiers, no card.

$ export PINAKES_API_KEY=pk_live_...
Get your key See the catalog →

Public reads need no key — add a pk_live_ key for an account. Everyone shares the same base rate limits while we’re in preview.

Biology today. The same deterministic engine, any corpus — named for the Pínakes, the first catalogue of the Library of Alexandria.