# paleobiology-mcp-server [Health: Active]
**Category:** 💻 Developer Tools
**Repository:** https://github.com/cyanheads/paleobiology-mcp-server
**GitHub Stars:** 2
**Views:** 0
**Installs:** 0
**Upvotes:** 0
**Directory Page:** https://allmcps.com/mcp/paleobiology-mcp-server
## Description
Search fossil occurrences, taxon ranges, diversity through deep time, and the geologic time scale.
## Claude Desktop Quick Installation
Install path detected from listing signals. Uses `bunx` (confidence: high):
```json
"mcpServers": {
"paleobiology-mcp-server": {
"command": "bunx",
"args": ["@cyanheads/paleobiology-mcp-server@latest"]
}
}
```
## Documentation & README
@cyanheads/paleobiology-mcp-server
Search fossil occurrences, resolve taxon fossil ranges, plot diversity through deep time, and look up the geologic time scale via MCP. STDIO or Streamable HTTP.
8 Tools • 2 Resources
[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/paleobiology-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/paleobiology-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
[](https://github.com/cyanheads/paleobiology-mcp-server/releases/latest/download/paleobiology-mcp-server.mcpb) [](https://cursor.com/en/install-mcp?name=paleobiology-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcGFsZW9iaW9sb2d5LW1jcC1zZXJ2ZXIiXX0=) [](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22paleobiology-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fpaleobiology-mcp-server%22%5D%7D)
[](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
**Public Hosted Server:** [https://paleobiology.caseyjhand.com/mcp](https://paleobiology.caseyjhand.com/mcp)
---
## 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.
| Tool Name | Description |
|:----------|:------------|
| `paleobiology_search_occurrences` | Search fossil occurrences by taxon, geologic time, geography, and depositional environment. Every row carries both modern and paleo coordinates. The flagship; broad results spill to a DataCanvas for SQL. |
| `paleobiology_get_taxon` | Resolve a taxon by name or `taxon_no` to its accepted name, rank, classification, parent, occurrence count, and first/last-appearance (FAD/LAD) range. Run first to resolve names for the other tools. |
| `paleobiology_get_diversity` | Compute a diversity / origination / extinction curve for a clade across geologic time, binned by period, epoch, or age. Returns the full bin set inline. |
| `paleobiology_list_intervals` | Look up the geologic time scale — eons through ages with absolute-age (Ma) boundaries and nesting. Translates named intervals ↔ Ma. Served offline from a bundled ICS snapshot; a name outside it costs one PBDB lookup across the sub-stage and regional scales. |
| `paleobiology_search_collections` | Find fossil collections (localities) by area and geologic time, with their formation, lithology, depositional environment, and co-occurring-fossils count. Paged inline. |
| `paleobiology_dataframe_query` | Run a read-only SQL `SELECT` over occurrence sets staged on a DataCanvas by `paleobiology_search_occurrences`. SELECT only. |
| `paleobiology_dataframe_describe` | List the tables and columns staged on a DataCanvas. Call before `paleobiology_dataframe_query` to discover table and column names. |
| `paleobiology_dataframe_drop` | Drop a single staged table to free memory before its TTL expires. Opt-in — registered only when `PALEOBIOLOGY_DATAFRAME_DROP_ENABLED=true`. |
---
### `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
- `base_id` filters the same clade by its resolved PBDB `taxon_no` — take it from `paleobiology_get_taxon` (or `accepted_no` on an occurrence row) and skip the name ambiguity. `base_name` and `base_id` are mutually exclusive; sending both is rejected at the tool boundary
- 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
- `lngmin`/`lngmax` are a closed pair (both or neither), and `min_ma` must be strictly less than `max_ma` — both are rejected at the tool boundary with a recovery hint, before the upstream request. A lone `latmin` or `latmax` is valid and filters as a half-plane
- 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, age interval, and higher classification (phylum through genus)
- Broad queries return many rows: an inline preview answers the immediate question, and when the set outgrows that preview the matching occurrences — up to the per-call cap (`limit`, further bounded by `PBDB_MAX_OCCURRENCES`) — stage on a DataCanvas for SQL via `paleobiology_dataframe_query`. `canvas_id` and `table_name` come back only on that spill path; a result that fits inline stages nothing
- Results page inline via `limit`/`offset` against the true upstream match count. When occurrences remain, the notice names the page bounds and the exact next offset (`Showing occurrences 1–500 of 4170. Advance offset to 500 for the next page.`); paging past the end reports the overshoot instead of blaming the filters
- 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
- The `taxon_no` it returns is the `base_id` accepted by `paleobiology_search_occurrences`, `paleobiology_get_diversity`, and `paleobiology_search_collections`
- `show_children` also lists immediate child taxa, up to 200 per call. `children_truncated` says whether more remain and `children_offset` says where the page started — advance `children_offset` by 200 while `children_truncated` is true to walk the whole child list. A taxon with over 200 immediate children returns a page, never a silently clipped list
- 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` **or** `base_id` (exactly one is required; both together, or neither, is rejected at the tool boundary), bound by a named interval (e.g. `Mesozoic`) or a `max_ma`/`min_ma` range (`min_ma` must be strictly less than `max_ma`)
- `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` or `base_id` (mutually exclusive), 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)
- Same bounding-box and Ma-ordering rules as `paleobiology_search_occurrences`: `lngmin`/`lngmax` both or neither, `min_ma` strictly less than `max_ma`
- 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
| Type | Name | Description |
|:---|:---|:---|
| Resource | `paleobiology://occurrence/{occurrence_no}` | One fossil occurrence with full detail — modern + paleo coordinates, classification, strata, locality, and the CC BY source credit. |
| Resource | `paleobiology://taxon/{taxon_no}` | One taxon record with its fossil range, classification, and the CC BY source credit. |
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`](https://www.npmjs.com/package/@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 the international scale's named intervals ↔ absolute Ma boundaries with no network call, and falls back to a PBDB lookup for the sub-stage and regional names that occurrence and collection rows report (`Late Maastrichtian`, `Lancian`), labeling each answer with its source and scale
- 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, roll up by family from the `classification` JSON column)
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`, every PBDB-backed tool and resource carries 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
### 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:
```json
{
"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:
```json
{
"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):
```json
{
"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:
```json
{
"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:
```sh
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](https://bun.sh/) or higher (or Node.js v24+).
- No API key — the Paleobiology Database is fully open.
### Installation
1. **Clone the repository:**
```sh
git clone https://github.com/cyanheads/paleobiology-mcp-server.git
```
2. **Navigate into the directory:**
```sh
cd paleobiology-mcp-server
```
3. **Install dependencies:**
```sh
bun install
```
4. **Configure environment (optional):**
```sh
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` | Hard cap on rows pulled per occurrence/collection call. | `1000` |
| `CANVAS_PROVIDER_TYPE` | Set to `duckdb` to enable the DataCanvas spill path and `paleobiology_dataframe_*` tools. | `none` |
| `PALEOBIOLOGY_DATAFRAME_DROP_ENABLED` | Register `paleobiology_dataframe_drop`. Absent from `tools/list` when unset. | `false` |
| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
| `MCP_HTTP_PORT` | Port for HTTP server. | `3010` |
| `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |
| `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |
| `OTEL_ENABLED` | Enable [OpenTelemetry instrumentation](https://github.com/cyanheads/mcp-ts-core/tree/main/docs/telemetry) (spans, metrics, completion logs). | `false` |
See [`.env.example`](https://github.com/cyanheads/paleobiology-mcp-server/blob/HEAD/.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
```sh
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`](https://github.com/cyanheads/paleobiology-mcp-server/blob/HEAD/CLAUDE.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:
```sh
bun run devcheck
bun run test
```
## License
Apache-2.0 — see [LICENSE](https://github.com/cyanheads/paleobiology-mcp-server/blob/HEAD/LICENSE) for details.
Data is from the [Paleobiology Database](https://paleobiodb.org), licensed CC BY 4.0 — credit it in downstream use.