paleobiology-mcp-server

<div align="center"> <h1>@cyanheads/paleobiology-mcp-server</h1> <p><b>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.</b> <div>7 Tools • 2 Resources</div> </p> </div> <div align="center"> [](./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/) </div> <div align="center"> [](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) </div> --- ## 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 from a bundled ICS snapshot; no network call. | | `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 - Age by a named interval (e.g. `Maastrichtian`) or a `max_ma`/`min_ma` range, and/or a lng/lat bounding box - `environment` enum: `marine`, `terrestrial`, `freshwater` - 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 full set stages on a DataCanvas (`canvas_id` + `table_name`) for SQL via `paleobiology_dataframe_query` - Reusing a `canvas_id` **replaces** that canvas's occurrence table — each search restages the full 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` - 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. | | Resource | `paleobiology://taxon/{taxon_no}` | One taxon record with its fossil range and classification. | 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 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: ```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`](./.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`](./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](LICENSE) for details. Data is from the [Paleobiology Database](https://paleobiodb.org), licensed CC BY 4.0 — credit it in downstream use.