paleobiology-mcp-server

---

Overview

Fossil biodiversity over the Paleobiology Database (PBDB), spanning roughly 540 million years. Resolve taxon fossil ranges, search fossil occurrences and collections by taxon, geologic time, and location, and plot diversity through deep time.

Tools

Tool	Description
paleobiology_search_occurrences	Search fossil occurrences by taxon, geologic time, geography, and depositional environment. Every row carries both modern and paleo coordinates; with DataCanvas on, broad results spill to a canvas for SQL.
paleobiology_get_taxon	Resolve a taxon by name or taxon_no to its accepted name, rank, classification, and FAD/LAD range — the name-resolution gateway.
paleobiology_get_diversity	Compute a diversity / origination / extinction curve for a clade across geologic time.
paleobiology_list_intervals	Look up the geologic time scale — named intervals ↔ absolute Ma boundaries.
paleobiology_search_collections	Find fossil collections (localities) by area, geologic time, formation, and lithology.
paleobiology_get_references	Resolve the reference_no on occurrence and collection rows to full citations — authors, year, title, publication, pages, DOI.
paleobiology_dataframe_query	Run a read-only SQL SELECT over occurrence sets staged on a DataCanvas. Listed only when DataCanvas is on.
paleobiology_dataframe_describe	List the tables and columns staged on a DataCanvas. Listed only when DataCanvas is on.
paleobiology_dataframe_drop	Drop a single staged table to free memory before its TTL expires. Opt-in; also needs DataCanvas.

Resources

Resource	Description
paleobiology://occurrence/{occurrence_no}	One fossil occurrence with full detail — modern + paleo coordinates, classification, strata, locality.
paleobiology://taxon/{taxon_no}	One taxon record with its fossil range and classification.
paleobiology://reference/{reference_no}	One bibliographic reference — the formatted citation plus its structured fields.

All resource data is also reachable via tools — the resources mirror a single-record read of paleobiology_search_occurrences / paleobiology_get_taxon / paleobiology_get_references for clients that surface resources. Tool-only clients lose nothing.

---

Capability reference

paleobiology_search_occurrences _tool

• Requires at least one taxon, time, geographic, environment, or collection_no filter. Use base_name or base_id for a clade, taxon_name for an exact match; page with limit (default 100, max 500 per call) and offset. Responses stay within 100,000 bytes, and the notice names the offset that continues
• Returns modern and paleo coordinates, named intervals and Ma ages, strata, and higher classification, with totalCount for PBDB's true match count. Errors: missing_filter, conflicting_taxon_filter, incomplete_bbox, inverted_ma_range, and pbdb_invalid_parameter (with PBDB's reason) for a value PBDB cannot use
• With DataCanvas on, a page too large to inline is staged on a canvas and returns canvas_id + table_name for paleobiology_dataframe_describe, then SQL. If the canvas cap is reached, it fails with retryable canvas_capacity_exhausted: pass an existing canvas_id or lower limit to the value the message names. Without DataCanvas, an overflowing page is cut

---

paleobiology_get_taxon _tool

• Resolve by name or taxon_no to accepted name, rank, classification, parent, occurrence count, and FAD/LAD range in Ma. The returned taxon_no is the base_id accepted by occurrence, diversity, and collection searches
• show_children adds up to 200 immediate child taxa per call; children_truncated and children_offset say whether and where to continue
• Typed errors: taxon_not_found, missing_selector, conflicting_selector when both name and taxon_no are sent

---

paleobiology_get_diversity _tool

• Requires a clade (base_name or base_id), optionally bounded by interval or max_ma/min_ma. Choose count (genera, species, families) and resolution (period, epoch, age); defaults are genera by period
• Returns the full bin set inline, oldest-first, with sampled, implied, origination, extinction, range-through, and occurrence counts
• Typed errors: missing_filter, conflicting_taxon_filter, inverted_ma_range, pbdb_invalid_parameter for a value PBDB cannot use (an unknown interval)

---

paleobiology_list_intervals _tool

• Filter by name, a min_ma/max_ma overlap window, or level (eon, era, period, epoch, age); omit filters to browse the bundled ICS scale
• Returns interval rank, Ma boundaries, parent_no, and an upstream scale where available. source (bundled_ics / pbdb_upstream) and snapshot_version identify the source; names outside the snapshot use PBDB
• Typed errors: interval_not_found for an unmatched name; retryable interval_lookup_unavailable when PBDB cannot resolve a name outside the snapshot; inverted_ma_range when max_ma is below min_ma

---

paleobiology_search_collections _tool

• Requires at least one taxon, time, geographic, formation, lithology, or environment filter. Page with limit (default 100, max 500 per call) and offset. Responses stay within 100,000 bytes, and the notice names the offset that continues
• Returns locality coordinates, age, strata, lithology, environment, and n_occs, with totals. Pass collection_no to paleobiology_search_occurrences for the fauna at that locality
• Typed errors: missing_filter, conflicting_taxon_filter, incomplete_bbox, inverted_ma_range, pbdb_invalid_parameter for a value PBDB cannot use (an unknown interval, or an unknown lithology sent as the only filter)

---

paleobiology_get_references _tool

• Pass 1–500 reference_nos from occurrence or collection rows; the first 25 distinct ids resolve in one PBDB request, and the rest come back in remaining_reference_nos for the next call
• Returns references in request order: the plain-text citation exactly as PBDB formats it, plus title, year, authors, editors, publication, volume, issue, pages, publisher, language, and doi where recorded
• Ids PBDB has no reference for land in not_found with a notice — a miss is a result, not an error

---

paleobiology_dataframe_query _tool

• Runs a read-only SQL SELECT against occurrence sets staged by paleobiology_search_occurrences, using the table_name it returned; writes and file-reading functions are rejected
• The classification column is JSON — roll up by rank with json_extract_string(classification, '$.family') (also $.phylum, $.class, $.order, $.genus)
• Responses stay within 100,000 bytes; the notice names the ORDER BY … LIMIT/OFFSET that reads the rest. truncated: true means row_count stopped at the canvas row cap
• Listed only when DataCanvas is on (CANVAS_PROVIDER_TYPE=duckdb)

---

paleobiology_dataframe_describe _tool

• Lists the tables staged on a canvas, each with its row count and column names/types/nullability — call before paleobiology_dataframe_query to discover identifiers
• Listed only when DataCanvas is on (CANVAS_PROVIDER_TYPE=duckdb)

---

paleobiology_dataframe_drop _tool

• Drops one staged table by canvas_id + table_name to free memory before its TTL expires; dropping a nonexistent table returns dropped: false, not an error
• Opt-in — needs DataCanvas on and PALEOBIOLOGY_DATAFRAME_DROP_ENABLED=true
• Typed error: canvas_not_found when the canvas has expired or never existed

---

paleobiology://occurrence/{occurrence_no} _resource

• Path param occurrence_no is a bare positive integer (regex-validated), from paleobiology_search_occurrences output
• Returns the same full occurrence detail as the tool — accepted/identified names, age, modern + paleo coordinates, formation/strata, locality — plus a CC BY 4.0 attribution field
• Typed error: occurrence_not_found

---

paleobiology://taxon/{taxon_no} _resource

• Path param taxon_no is a bare positive integer (regex-validated), from paleobiology_get_taxon or an occurrence's accepted_no
• Mirrors paleobiology_get_taxon's shape exactly — accepted name, rank, classification, parent, FAD/LAD range — plus a CC BY 4.0 attribution field
• Typed error: taxon_not_found

---

paleobiology://reference/{reference_no} _resource

• Path param reference_no is a bare positive integer (regex-validated), from an occurrence or collection row
• Returns the same record as one paleobiology_get_references entry plus a CC BY 4.0 attribution field
• Typed error: reference_not_found

---

Features

Built on @cyanheads/mcp-ts-core: stdio and Streamable HTTP transports, pluggable auth (none / jwt / oauth), swappable storage (in-memory, filesystem, Supabase, Cloudflare KV/R2/D1), structured logging with optional OpenTelemetry tracing.

PBDB-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 the international scale's named intervals ↔ absolute Ma boundaries with no network call, falling back to a PBDB lookup for sub-stage and regional names
• Optional DataCanvas spill for broad occurrence queries (CANVAS_PROVIDER_TYPE=duckdb): an inline preview plus a staged table queryable with read-only SQL (count by interval, group by formation/country, roll up by family from the classification JSON column)
• No auth, no API key — PBDB is fully open (MCP_AUTH_MODE defaults to none)
• Diversity counts reflect sampling and collection effort, not true past diversity

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 on every row: reference_no for paleobiology_get_references, plus CC BY attribution on tools and resources
• Sparse upstream fields (paleo-coords, formation, late_interval) are omitted rather than zeroed

---

Getting started

Public Hosted Instance

A public instance is available at https://paleobiology.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:

{
  "mcpServers": {
    "paleobiology-mcp-server": {
      "type": "streamable-http",
      "url": "https://paleobiology.caseyjhand.com/mcp"
    }
  }
}

Self-Hosted / Local

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, and the paleobiology_dataframe_* tools are left off tools/list (the HTTP landing page shows them as disabled, with the setting that enables them).

Prerequisites

• Bun v1.4 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.

Variable	Description	Default
PBDB_BASE_URL	Paleobiology Database API base. Override for a mirror/proxy or pinned API version.	https://paleobiodb.org/data1.2
PBDB_TIMEOUT_MS	Per-request timeout in milliseconds. Diversity queries over large clades can be slow.	30000
PBDB_MAX_OCCURRENCES	Cap on rows pulled per occurrence/collection call (tools pull at most 500, so only a lower value matters).	1000
CANVAS_PROVIDER_TYPE	Set to duckdb to enable the DataCanvas spill path and list the paleobiology_dataframe_* tools.	none
PALEOBIOLOGY_DATAFRAME_DROP_ENABLED	Enable paleobiology_dataframe_drop (DataCanvas must also be on).	false
MCP_TRANSPORT_TYPE	Transport: stdio or http.	stdio
MCP_HTTP_PORT	Port for HTTP server.	3010
MCP_SESSION_MODE	HTTP session mode: stateless, stateful, or auto.	stateless
MCP_AUTH_MODE	Auth mode: none, jwt, or oauth.	none
MCP_LOG_LEVEL	Log level (RFC 5424).	info
OTEL_ENABLED	Enable OpenTelemetry instrumentation (spans, metrics, completion logs).	false
OTEL_EXPORTER_OTLP_ENDPOINT	Base OTLP URL for traces and metrics. Logs require their own endpoint.	unset
OTEL_EXPORTER_OTLP_LOGS_ENDPOINT	Enable OTLP log export to this exact URL.	unset
LOG_TOOL_FAILURE_PAYLOADS	Log failed tool arguments and results, with key-name redaction; secrets in free-form values remain.	false
LOG_TOOL_FAILURE_PAYLOAD_MAX_BYTES	UTF-8 byte cap per logged payload.	16384

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

Running the server

Local development

• Build and run:

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

• Run checks and tests:

  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

Directory	Purpose
src/index.ts	createApp() entry point — registers tools/resources and inits services.
src/config	Server-specific environment variable parsing and validation with Zod.
src/mcp-server/tools	Tool definitions (*.tool.ts).
src/mcp-server/resources	Resource definitions (*.resource.ts).
src/services/pbdb	Paleobiology Database HTTP client, normalization, and domain types.
src/services/intervals	In-memory index over the bundled ICS geologic time-scale snapshot.
tests/	Unit and integration tests mirroring src/.

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)

Data attribution

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

Contributing

Issues are welcome. Run checks and tests before submitting:

bun run devcheck
bun run test

License

Apache-2.0 — see LICENSE for details.