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\n

@cyanheads/paleobiology-mcp-server

\n

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.\n

8 Tools • 2 Resources
\n

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\n\n[![Version](https://img.shields.io/badge/Version-0.3.7-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/paleobiology-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.2.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/paleobiology-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/paleobiology-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.2%2B-blueviolet.svg?style=flat-square)](https://bun.sh/)\n\n
\n\n
\n\n[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/paleobiology-mcp-server/releases/latest/download/paleobiology-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=paleobiology-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcGFsZW9iaW9sb2d5LW1jcC1zZXJ2ZXIiXX0=) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](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)\n\n[![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)\n\n
\n\n
\n\n**Public Hosted Server:** [https://paleobiology.caseyjhand.com/mcp](https://paleobiology.caseyjhand.com/mcp)\n\n
\n\n---\n\n## Overview\n\nFossil 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 from any MCP client. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.\n\n### Tools\n\n| Tool | Description |\n|:---|:---|\n| `paleobiology_search_occurrences` | Search fossil occurrences by taxon, geologic time, geography, and depositional environment. Every row carries both modern and paleo coordinates; broad results spill to a DataCanvas for SQL. |\n| `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. |\n| `paleobiology_get_diversity` | Compute a diversity / origination / extinction curve for a clade across geologic time. |\n| `paleobiology_list_intervals` | Look up the geologic time scale — named intervals ↔ absolute Ma boundaries. |\n| `paleobiology_search_collections` | Find fossil collections (localities) by area, geologic time, formation, and lithology. |\n| `paleobiology_dataframe_query` | Run a read-only SQL `SELECT` over occurrence sets staged on a DataCanvas. |\n| `paleobiology_dataframe_describe` | List the tables and columns staged on a DataCanvas. |\n| `paleobiology_dataframe_drop` | Drop a single staged table to free memory before its TTL expires. Opt-in. |\n\n### Resources\n\n| Resource | Description |\n|:---|:---|\n| `paleobiology://occurrence/{occurrence_no}` | One fossil occurrence with full detail — modern + paleo coordinates, classification, strata, locality. |\n| `paleobiology://taxon/{taxon_no}` | One taxon record with its fossil range and classification. |\n\nAll 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.\n\n---\n\n## Capability reference\n\n### `paleobiology_search_occurrences` tool\n\n- 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) and `offset`\n- Returns modern and paleo coordinates, named intervals and Ma ages, strata, and higher classification. `totalCount` and the notice report PBDB's true match count and next offset; rejected filters carry `missing_filter`, `conflicting_taxon_filter`, `incomplete_bbox`, or `inverted_ma_range`\n- Large pages spill to DataCanvas and return `canvas_id` + `table_name` for SQL. Reusing a `canvas_id` replaces that canvas's occurrence table; a page that fits inline stages nothing\n\n---\n\n### `paleobiology_get_taxon` tool\n\n- 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\n- `show_children` adds up to 200 immediate child taxa per call; `children_truncated` and `children_offset` say whether and where to continue\n- Typed errors: `taxon_not_found`, `missing_selector`\n\n---\n\n### `paleobiology_get_diversity` tool\n\n- 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\n- Returns the full bin set inline, oldest-first, with sampled, implied, origination, extinction, range-through, and occurrence counts\n- Typed errors: `missing_filter`, `conflicting_taxon_filter`, `inverted_ma_range`\n\n---\n\n### `paleobiology_list_intervals` tool\n\n- 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\n- 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\n- Typed errors: `interval_not_found` for an unmatched name; retryable `interval_lookup_unavailable` when PBDB cannot resolve a name outside the snapshot\n\n---\n\n### `paleobiology_search_collections` tool\n\n- Requires at least one taxon, time, geographic, `formation`, `lithology`, or `environment` filter. Page with `limit` (default 100, max 500) and `offset`\n- Returns locality coordinates, age, strata, lithology, environment, and `n_occs`, with totals and truncation guidance. Pass `collection_no` to `paleobiology_search_occurrences` for the fauna at that locality\n- Typed errors: `missing_filter`, `conflicting_taxon_filter`, `incomplete_bbox`, `inverted_ma_range`\n\n---\n\n### `paleobiology_dataframe_query` tool\n\n- Runs a read-only SQL `SELECT` against occurrence sets staged on a DataCanvas by `paleobiology_search_occurrences`; writes and file-reading functions are rejected\n- Reference tables by the `table_name` a spilled search returned; the `classification` column is JSON — roll up by rank with `json_extract_string(classification, '$.family')` (also `$.phylum`, `$.class`, `$.order`, `$.genus`)\n- Output caps at the canvas row limit; `truncated: true` marks a trimmed result\n- Typed error: `canvas_disabled` when `CANVAS_PROVIDER_TYPE` is not `duckdb`\n\n---\n\n### `paleobiology_dataframe_describe` tool\n\n- 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\n- Typed error: `canvas_disabled` when `CANVAS_PROVIDER_TYPE` is not `duckdb`\n\n---\n\n### `paleobiology_dataframe_drop` tool\n\n- 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\n- Opt-in — callable only when `PALEOBIOLOGY_DATAFRAME_DROP_ENABLED=true`, absent from `tools/list` otherwise; the manifest retains its enable hint\n- Typed error: `canvas_disabled` when `CANVAS_PROVIDER_TYPE` is not `duckdb`\n\n---\n\n### `paleobiology://occurrence/{occurrence_no}` resource\n\n- Path param `occurrence_no` is a bare positive integer (regex-validated), from `paleobiology_search_occurrences` output\n- 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\n- Typed error: `occurrence_not_found`\n\n---\n\n### `paleobiology://taxon/{taxon_no}` resource\n\n- Path param `taxon_no` is a bare positive integer (regex-validated), from `paleobiology_get_taxon` or an occurrence's `accepted_no`\n- Mirrors `paleobiology_get_taxon`'s shape exactly — accepted name, rank, classification, parent, FAD/LAD range — plus a CC BY 4.0 `attribution` field\n- Typed error: `taxon_not_found`\n\n---\n\n## Features\n\nBuilt on [`@cyanheads/mcp-ts-core`](https://github.com/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.\n\nPBDB-specific:\n\n- 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\n- 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\n- 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)\n- No auth, no API key — PBDB is fully open (`MCP_AUTH_MODE` defaults to `none`)\n- PBDB's accepted taxonomy may differ from the searched name or other backbones. Diversity counts reflect sampling and collection effort, rather than true past diversity\n\nAgent-friendly output:\n\n- 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\n- Both temporal representations on every age — the named interval **and** its Ma boundaries\n- 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\n\n---\n\n## Getting started\n\n### Public Hosted Instance\n\nA public instance is available at `https://paleobiology.caseyjhand.com/mcp` — no installation required. Point any MCP client at it via Streamable HTTP:\n\n```json\n{\n \"mcpServers\": {\n \"paleobiology-mcp-server\": {\n \"type\": \"streamable-http\",\n \"url\": \"https://paleobiology.caseyjhand.com/mcp\"\n }\n }\n}\n```\n\n### Self-Hosted / Local\n\nAdd one of the following to your MCP client configuration file. PBDB is keyless — no API key required.\n\nWith bunx:\n\n```json\n{\n \"mcpServers\": {\n \"paleobiology-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"bunx\",\n \"args\": [\"@cyanheads/paleobiology-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\"\n }\n }\n }\n}\n```\n\nOr with npx (no Bun required):\n\n```json\n{\n \"mcpServers\": {\n \"paleobiology-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"npx\",\n \"args\": [\"-y\", \"@cyanheads/paleobiology-mcp-server@latest\"],\n \"env\": {\n \"MCP_TRANSPORT_TYPE\": \"stdio\",\n \"MCP_LOG_LEVEL\": \"info\"\n }\n }\n }\n}\n```\n\nOr with Docker:\n\n```json\n{\n \"mcpServers\": {\n \"paleobiology-mcp-server\": {\n \"type\": \"stdio\",\n \"command\": \"docker\",\n \"args\": [\n \"run\", \"-i\", \"--rm\",\n \"-e\", \"MCP_TRANSPORT_TYPE=stdio\",\n \"ghcr.io/cyanheads/paleobiology-mcp-server:latest\"\n ]\n }\n }\n}\n```\n\nFor Streamable HTTP, set the transport and start the server:\n\n```sh\nMCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http\n# Server listens at http://localhost:3010/mcp\n```\n\nTo 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.\n\n### Prerequisites\n\n- [Bun v1.4](https://bun.sh/) or higher (or Node.js v24+).\n- No API key — the Paleobiology Database is fully open.\n\n### Installation\n\n1. **Clone the repository:**\n\n```sh\ngit clone https://github.com/cyanheads/paleobiology-mcp-server.git\n```\n\n2. **Navigate into the directory:**\n\n```sh\ncd paleobiology-mcp-server\n```\n\n3. **Install dependencies:**\n\n```sh\nbun install\n```\n\n4. **Configure environment (optional):**\n\n```sh\ncp .env.example .env\n# edit .env to override defaults — all vars are optional\n```\n\n## Configuration\n\nAll variables are optional — the server runs with no configuration against the public PBDB API.\n\n| Variable | Description | Default |\n|:---------|:------------|:--------|\n| `PBDB_BASE_URL` | Paleobiology Database API base. Override for a mirror/proxy or pinned API version. | `https://paleobiodb.org/data1.2` |\n| `PBDB_TIMEOUT_MS` | Per-request timeout in milliseconds. Diversity queries over large clades can be slow. | `30000` |\n| `PBDB_MAX_OCCURRENCES` | Hard cap on rows pulled per occurrence/collection call. | `1000` |\n| `CANVAS_PROVIDER_TYPE` | Set to `duckdb` to enable the DataCanvas spill path and `paleobiology_dataframe_*` tools. | `none` |\n| `PALEOBIOLOGY_DATAFRAME_DROP_ENABLED` | Enable `paleobiology_dataframe_drop`. Absent from `tools/list` when unset; the manifest retains its enable hint. | `false` |\n| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |\n| `MCP_HTTP_PORT` | Port for HTTP server. | `3010` |\n| `MCP_SESSION_MODE` | HTTP session posture: `stateless`, `stateful`, or `auto`. The server declares `stateless` in `src/index.ts` — it holds no per-session state — and this variable overrides that declaration. | `stateless` |\n| `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |\n| `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |\n| `OTEL_ENABLED` | Enable [OpenTelemetry instrumentation](https://github.com/cyanheads/mcp-ts-core/tree/main/docs/telemetry) (spans, metrics, completion logs). | `false` |\n| `OTEL_EXPORTER_OTLP_ENDPOINT` | Base OTLP URL for traces and metrics. Logs require their own endpoint. | unset |\n| `OTEL_EXPORTER_OTLP_LOGS_ENDPOINT` | Enable OTLP log export to this exact URL. | unset |\n| `LOG_TOOL_FAILURE_PAYLOADS` | Log failed tool arguments and results, with key-name redaction; secrets in free-form values remain. | `false` |\n| `LOG_TOOL_FAILURE_PAYLOAD_MAX_BYTES` | UTF-8 byte cap per logged payload. | `16384` |\n\nSee [`.env.example`](./.env.example) for the full list of optional overrides.\n\n## Running the server\n\n### Local development\n\n- **Build and run:**\n\n ```sh\n # One-time build\n bun run rebuild\n\n # Run the built server\n bun run start:stdio\n # or\n bun run start:http\n ```\n\n- **Run checks and tests:**\n\n ```sh\n bun run devcheck # Lint, format, typecheck, security\n bun run test # Vitest test suite\n bun run lint:mcp # Validate MCP definitions against spec\n ```\n\n### Docker\n\n```sh\ndocker build -t paleobiology-mcp-server .\ndocker run --rm -p 3010:3010 paleobiology-mcp-server\n```\n\nThe 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.\n\n## Project structure\n\n| Directory | Purpose |\n|:----------|:--------|\n| `src/index.ts` | `createApp()` entry point — registers tools/resources and inits services. |\n| `src/config` | Server-specific environment variable parsing and validation with Zod. |\n| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). |\n| `src/mcp-server/resources` | Resource definitions (`*.resource.ts`). |\n| `src/services/pbdb` | Paleobiology Database HTTP client, normalization, and domain types. |\n| `src/services/intervals` | In-memory index over the bundled ICS geologic time-scale snapshot. |\n| `tests/` | Unit and integration tests mirroring `src/`. |\n\n## Development guide\n\nSee [`CLAUDE.md`/`AGENTS.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:\n\n- Handlers throw, framework catches — no `try/catch` in tool logic\n- Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage\n- Register new tools and resources via the barrels in `src/mcp-server/*/definitions/index.ts`\n- 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`)\n\n## Data attribution\n\nData is from the [Paleobiology Database](https://paleobiodb.org), licensed CC BY 4.0 — credit it in downstream use.\n\n## Contributing\n\nIssues are welcome. Run checks and tests before submitting:\n\n```sh\nbun run devcheck\nbun run test\n```\n\n## License\n\nApache-2.0 — see [LICENSE](LICENSE) for details.\n","readmeFilename":"README.md"}