paleobiology-mcp-server

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  <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>8 Tools • 2 Resources</div>
  </p>
</div>

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---

## 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 [`@cyanhe