io.github.cyanheads/paleobiology-mcp-server

Tools

Eight tools (seven by default) — five domain tools for the Paleobiology Database, plus a DataCanvas trio for SQL over staged occurrence sets. Large occurrence results spill to a canvas; the other domain tools return inline.

paleobiology_search_occurrences

Search fossil occurrences filtered by taxon, geologic time, geography, and environment — the flagship.

• base_name (a clade and all its descendants) or taxon_name (exact) for the taxon filter
• Age by a named interval (e.g. Maastrichtian) or a max_ma/min_ma range, and/or a lng/lat bounding box
• collection_no scopes the search to a single locality — drill from a paleobiology_search_collections row into the fauna found there
• environment enum: marine, terrestrial, freshwater
• At least one filter (taxon, time, place, environment, or collection_no) is required — an unfiltered call is rejected before the upstream request, not reported as PBDB being unavailable
• Every row carries two distinct coordinate systems — modern lng/lat (where the rock is today) and paleo lng/lat (where the landmass sat at deposition) — plus formation and age interval
• Broad queries return many rows: an inline preview answers the immediate question, and the matching occurrences — up to the per-call cap (limit, further bounded by PBDB_MAX_OCCURRENCES) — stage on a DataCanvas (canvas_id + table_name) for SQL via paleobiology_dataframe_query. The response notice flags when the cap was hit and more may match upstream
• Reusing a canvas_id replaces that canvas's occurrence table — each search restages its result, it does not accumulate across calls

paleobiology_get_taxon

Resolve a taxon by name or integer taxon_no to its full record and fossil temporal range — the name-resolution gateway the occurrence and diversity tools depend on.

• Returns accepted name, rank, higher classification, immediate parent, occurrence count, and FAD/LAD range in Ma
• show_children also lists immediate child taxa
• PBDB taxonomy is opinionated and can differ from GBIF's backbone, so the accepted name may differ from the searched name — the response surfaces both

paleobiology_get_diversity

Compute a diversity / origination / extinction curve for a clade across geologic time.

• Clade-inclusive base_name, bound by a named interval (e.g. Mesozoic) or a max_ma/min_ma range
• count enum: genera, species, families; resolution enum: period, epoch, age
• The full bin set returns inline (a diversity series is a bounded set of geologic intervals)
• Counts reflect sampled diversity, biased by collection effort and rock availability — not true past diversity

paleobiology_search_collections

Find fossil collections (localities) by area and geologic time — "what has been dug up here, and from what rock."

• Each locality returns location, age (named interval and Ma), formation and strata, lithology, depositional environment, and co-occurring-fossils count
• Filter by base_name, a named interval or max_ma/min_ma range, a lng/lat bounding box, a formation or lithology name, and/or environment — at least one filter is required (an unfiltered call is rejected before the upstream request)
• Results page inline via limit/offset; the response discloses when more remain
• Take a collection_no from a row — or the same bbox+interval — into paleobiology_search_occurrences to see the fauna found together

Resources and prompts

All resource data is also reachable via tools — the resources mirror a single-record read of paleobiology_search_occurrences / paleobiology_get_taxon for clients that surface resources. Tool-only clients lose nothing. occurrence_no and taxon_no are bare integers from those tools' output.

Features

Built on @cyanheads/mcp-ts-core:

• Declarative tool, resource, and prompt definitions — single file per primitive, framework handles registration and validation
• Unified error handling — handlers throw, framework catches, classifies, and formats
• Pluggable auth: none, jwt, oauth (runs none by default — PBDB is keyless)
• Swappable storage backends: in-memory, filesystem, Supabase, Cloudflare KV/R2/D1
• Structured logging with optional OpenTelemetry tracing
• STDIO and Streamable HTTP transports

Paleobiology-specific:

• Type-safe client for the Paleobiology Database (PBDB) REST API, requesting vocab=pbdb so readable field names come straight from upstream instead of hand-mapped terse codes
• Bundled ICS geologic time-scale snapshot — paleobiology_list_intervals resolves named intervals ↔ absolute Ma boundaries with no network call
• DataCanvas spill for broad occurrence queries: an inline preview plus a staged table queryable with read-only SQL (count by interval, group by formation/country/lithology)

Agent-friendly output:

• Two coordinate systems on every occurrence — modern lng/lat and paleo lng/lat — distinctly labeled, so an agent never plots a deep-time fossil on a modern coastline
• Both temporal representations on every age — the named interval and its Ma boundaries
• Provenance and honesty — every row carries its reference_no, responses carry the CC-BY attribution, sparse upstream fields (paleo-coords, formation, late_interval) are omitted rather than zeroed, and diversity counts are flagged as sampled

Getting started

Add one of the following to your MCP client configuration file. PBDB is keyless — no API key required.

With bunx:

{
  "mcpServers": {
    "paleobiology-mcp-server": {
      "type": "stdio",
      "command": "bunx",
      "args": ["@cyanheads/paleobiology-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with npx (no Bun required):

{
  "mcpServers": {
    "paleobiology-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": ["-y", "@cyanheads/paleobiology-mcp-server@latest"],
      "env": {
        "MCP_TRANSPORT_TYPE": "stdio",
        "MCP_LOG_LEVEL": "info"
      }
    }
  }
}

Or with Docker:

{
  "mcpServers": {
    "paleobiology-mcp-server": {
      "type": "stdio",
      "command": "docker",
      "args": [
        "run", "-i", "--rm",
        "-e", "MCP_TRANSPORT_TYPE=stdio",
        "ghcr.io/cyanheads/paleobiology-mcp-server:latest"
      ]
    }
  }
}

For Streamable HTTP, set the transport and start the server:

MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcp

To enable SQL over large occurrence sets, set CANVAS_PROVIDER_TYPE=duckdb (the @duckdb/node-api peer dep ships in dependencies). Without it, paleobiology_search_occurrences still returns its inline preview; the paleobiology_dataframe_* tools fail with a clear "canvas disabled" message.

Prerequisites

• Bun v1.3 or higher (or Node.js v24+).
• No API key — the Paleobiology Database is fully open.

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/paleobiology-mcp-server.git

2. Navigate into the directory:

cd paleobiology-mcp-server

3. Install dependencies:

bun install

4. Configure environment (optional):

cp .env.example .env
# edit .env to override defaults — all vars are optional

Configuration

All variables are optional — the server runs with no configuration against the public PBDB API.

See .env.example for the full list of optional overrides.

Running the server

Local development

• Build and run:

  sh

  # One-time build
  bun run rebuild
  
  # Run the built server
  bun run start:stdio
  # or
  bun run start:http
  

• Run checks and tests:

  sh

  bun run devcheck   # Lint, format, typecheck, security
  bun run test       # Vitest test suite
  bun run lint:mcp   # Validate MCP definitions against spec
  

Docker

docker build -t paleobiology-mcp-server .
docker run --rm -p 3010:3010 paleobiology-mcp-server

The Dockerfile defaults to HTTP transport, stateless session mode, and logs to /var/log/paleobiology-mcp-server. OpenTelemetry peer dependencies are installed by default — build with --build-arg OTEL_ENABLED=false to omit them.

Project structure

Development guide

See CLAUDE.md/AGENTS.md for development guidelines and architectural rules. The short version:

• Handlers throw, framework catches — no try/catch in tool logic
• Use ctx.log for request-scoped logging, ctx.state for tenant-scoped storage
• Register new tools and resources via the barrels in src/mcp-server/*/definitions/index.ts
• Wrap external API calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields (a missing paleo-coordinate is "unknown", not 0,0)

Contributing

Issues and pull requests are welcome. Run checks and tests before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.

Data is from the Paleobiology Database, licensed CC BY 4.0 — credit it in downstream use.