# io.github.cyanheads/paleobiology-mcp-server (npm · @cyanheads/paleobiology-mcp-server)

Search fossil occurrences, taxon ranges, diversity through deep time, and the geologic time scale.

- Trust score: 65/100 (medium)
- Change this week: +56
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-08-07

## Components

- npm · `@cyanheads/paleobiology-mcp-server`: 65/100 (this document), [markdown](https://verifymcp.io/servers/cyanheads-paleobiology-mcp-server/cyanheads-paleobiology-mcp-server.md), [page](https://verifymcp.io/servers/cyanheads-paleobiology-mcp-server/cyanheads-paleobiology-mcp-server)

## Channel facts

- Registry: `npm`
- Package: `@cyanheads/paleobiology-mcp-server`
- Version: `0.3.4`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-08-07.

- **Supply Chain Security**: 98/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - 40 of 138 dependencies flagged as unhealthy.
- **Provenance & Transparency**: 45/100
  - Source repository is publicly reachable at the declared URL.
  - Provenance check failed: no build-provenance attestation is published.
  - Clear OSI-approved license (Apache-2.0).
  - Actively maintained (last published 7 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 59/100
  - AI-judged instruction clarity (excellent).
  - Context-footprint check failed: tool/resource definitions use about 3338 tokens (~476/item across 7 items; 7 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 0/100
  - Stability not yet verified: not enough scan history yet (needs a 30-day window).
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
  - Structured output schemas are declared (100% of tools); any adoption earns full credit.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

**Unverified: 1 category.** A category scored 0 because we could not verify it: a data source with nothing on this package, evidence we could not reach, or a check we could not run. We only credit what we can confirm.

## Install

### Claude

```bash
claude mcp add cyanheads-paleobiology-mcp-server -- npx -y @cyanheads/paleobiology-mcp-server
```

### Codex

```bash
codex mcp add cyanheads-paleobiology-mcp-server -- npx -y @cyanheads/paleobiology-mcp-server
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "cyanheads-paleobiology-mcp-server": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@cyanheads/paleobiology-mcp-server"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add cyanheads-paleobiology-mcp-server --command npx --arg -y --arg @cyanheads/paleobiology-mcp-server
```

### Hermes

```yaml
mcp_servers:
  cyanheads-paleobiology-mcp-server:
    command: "npx"
    args: ["-y", "@cyanheads/paleobiology-mcp-server"]
```

### Other

```json
{
  "mcpServers": {
    "cyanheads-paleobiology-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/paleobiology-mcp-server"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-08-07 (score 65, +3)

- [security improvement] Known CVEs: partial → pass
- [functional] Dependency health: partial → 0.87

### 2026-08-05 (score 62, +27)

- [security] Stability: Stability not yet verified: not enough scan history yet (needs a 30-day window).
- [functional improvement] MCP protocol: unverified → pass
- [functional improvement] Tool coverage: unverified → 100
- [functional] First check of Schema quality: fail
- [functional] First check of Tool coverage: 100
- [functional] First check of Schema quality: fail
- [functional] First check of Schema quality: excellent
- [functional] First check of Tool coverage: 100

### 2026-08-02 (score 35, +22)

- [security regression] Provenance: fail → unverified
- [security regression] Install scripts: pass → unverified
- [security improvement] Known CVEs: unverified → partial
- [security improvement] Malware scan: unverified → pass
- [security] Stability: Stability not yet verified: we do not have a sandbox capture of the MCP schema this version of the package serves yet.
- [functional regression] License: pass → unverified
- [functional regression] Maintenance: pass → unverified
- [functional improvement] Dependency health: unverified → partial
- [functional] Schema quality: Schema quality not yet verified: we do not have a sandbox capture of the MCP schema this version of the package serves yet.
- [functional] Capabilities: Protocol version not yet verified: we do not have a sandbox capture of the MCP handshake this version of the package performs yet.
- [functional] Tool coverage: Tool coverage not yet verified: we do not have a sandbox capture of the tool definitions this version of the package serves yet.
- [functional] Licence: Apache-2.0

### 2026-08-01 (score 13, +4)

- [functional] We updated how we score, so this day's move reflects our rubric, not a change to the server

### 2026-07-30 (score 9, −15)

- [security regression] Malware scan: pass → unverified
- [functional improvement] Dependency health: unverified → partial
- [functional] Schema quality: Schema quality not yet verified: our sandbox run of this package did not complete, so we have no schema to assess.
- [functional] Tool coverage: Tool coverage not yet verified: our sandbox run of this package did not complete, so we have no tool definitions to assess.
- [functional] Package version: 0.3.0 → 0.3.4

### 2026-07-28 (score 24, 0)

- [functional] Tool coverage: Tool coverage not yet verified: we do not have a sandbox capture of the tool definitions this version of the package serves yet.
- [functional] Schema quality: Schema quality not yet verified: we do not have a sandbox capture of the MCP schema this version of the package serves yet.

### 2026-07-27 (score 24)

First indexed and scored.

## MCP tools (7)

### `paleobiology_search_occurrences` (~1002 tokens)

paleobiology-mcp-server: search fossil occurrences

Search fossil occurrences filtered by taxon, geologic time, geography, and depositional environment — the flagship. Use base_name for a clade and all its descendants (what "Tyrannosaurus occurrences" usually means), base_id for that same clade by resolved taxon id, or taxon_name for an exact taxon. Bound the age by a named interval (e.g. "Maastrichtian") or a max_ma/min_ma range, and/or a lng/lat bounding box; scope to a single locality with collection_no (take it from a paleobiology_search_collections row). At least one filter is required — taxon, time, place, environment, or collection_no. 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 the formation, age interval, and higher classification (phylum through genus); never plot a deep-time occurrence on a modern coastline. Resolve a name with paleobiology_get_taxon first if unsure. 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 — stage on a DataCanvas (canvas_id + table_name, returned only then) for SQL via paleobiology_dataframe_query (count by interval, group by formation/country, map by region). The response reports how many occurrences matched in total, which rows this page covers, and the offset that reaches the next page — page through the whole match set with limit/offset.

Input parameters:

- `base_id` (integer): Clade-inclusive taxon filter by PBDB taxon id — the taxon_no from paleobiology_get_taxon, or accepted_no on an occurrence row. Same clade-inclusive semantics as base_name, but unambiguous where a nam…
- `base_name` (string): Clade-inclusive taxon filter — this taxon and all descendants, e.g. "Dinosauria". The usual choice. Supply this or base_id, never both.
- `canvas_id` (string): Canvas id from a prior call to re-stage onto the same workspace. Reusing it REPLACES (overwrites) the prior occurrence table — each search restages the full result, it does not append to or accumulat…
- `collection_no` (integer): Restrict to one collection (locality) by its PBDB collection_no — the fauna found together at that site. Take the id from a paleobiology_search_collections row to drill from a locality into its occur…
- `environment` (string): Depositional environment: "marine", "terrestrial", or "freshwater" (lacustrine + fluvial). Omit for all.
- `interval` (string): Named geologic interval bounding the age, e.g. "Cretaceous" or "Maastrichtian". Alternative to max_ma/min_ma.
- `latmax` (number): Northern edge of the bounding box, decimal degrees (−90…90). Valid on its own — a lone latitude edge filters as a half-plane.
- `latmin` (number): Southern edge of the bounding box, decimal degrees (−90…90). Valid on its own — a lone latitude edge filters as a half-plane.
- `limit` (integer): Maximum occurrences to pull per page (1–500). Caps the pull (further bounded by PBDB_MAX_OCCURRENCES); broad queries stage that page on the canvas for SQL. Pair with offset to walk the whole match se…
- `lngmax` (number): Eastern edge of the bounding box, decimal degrees (−180…180). Longitude is a closed pair — supply lngmin with it or neither.
- `lngmin` (number): Western edge of the bounding box, decimal degrees (−180…180). Longitude is a closed pair — supply lngmax with it or neither.
- `max_ma` (number): Older age bound in millions of years ago. Alternative to interval. When paired with min_ma it must be strictly greater — max_ma is the deeper-time end of the window.
- `min_ma` (number): Younger age bound in millions of years ago. Alternative to interval. When paired with max_ma it must be strictly smaller — min_ma is the nearer-to-present end of the window.
- `offset` (integer): Number of matching occurrences to skip before this page — page with limit by advancing offset. The response notice names the exact offset that reaches the next page.
- `taxon_name` (string): Exact taxon filter — only this taxon, not descendants. Use instead of base_name when you want a single taxon.

Output parameters:

- `attribution` (string): CC-BY data attribution for the Paleobiology Database.
- `canvas_id` (string): Canvas id holding the staged occurrence set — pass to paleobiology_dataframe_query. Present only when spilled is true; a result that fit inline stages nothing, so there is no table to query.
- `notice` (string): Guidance when no occurrence matched, when results spilled to the canvas, when occurrences remain past this page (naming the offset that reaches the next one), when offset ran past the end of the matc…
- `occurrences` (array): Inline preview of matching occurrences for the requested page. The staged occurrence set is on the canvas when spilled is true — it is one page of the match set rather than every match (the notice st…
- `row_count` (number): Rows staged on the canvas when spilled; otherwise the preview length. Capped at the per-call limit (PBDB_MAX_OCCURRENCES) — compare against the totalCount enrichment for how many matched upstream.
- `spilled` (boolean): True when the result exceeded the inline preview and the staged occurrence set was written to the canvas.
- `table_name` (string): Canvas table holding the staged occurrence set. Present only when spilled is true.
- `totalCount` (number): Total occurrences matching the filters upstream — the number this call was drawn from, which may exceed the staged set.

### `paleobiology_get_taxon` (~339 tokens)

paleobiology-mcp-server: get taxon record and fossil range

Resolve a taxon by name (e.g. "Tyrannosaurus") or by integer taxon_no to its accepted name, rank, higher classification, immediate parent, fossil occurrence count, and first/last appearance (FAD/LAD) range in millions of years — "when did this clade exist, and what is it." Run this first to resolve a name into the accepted name and taxon_no, then pass that id as base_id to paleobiology_search_occurrences, paleobiology_get_diversity, or paleobiology_search_collections for a clade-inclusive filter that carries no name ambiguity (the same id also appears as accepted_no on occurrence rows). Set show_children to also list immediate child taxa. PBDB taxonomy is opinionated and can differ from GBIF's backbone, so the accepted name may differ from the name you searched.

Input parameters:

- `children_offset` (integer): Number of immediate children to skip before the returned page — used only when show_children is true. Advance it by 200 while children_truncated is true to walk the whole child list.
- `name` (string): Taxon name to resolve, e.g. "Tyrannosaurus" or "Ammonoidea". Provide this or taxon_no.
- `show_children` (boolean): When true, include a page of the immediate child taxa of this taxon (at most 200 per call — children_truncated says whether more remain).
- `taxon_no` (integer): PBDB taxon id from a prior get_taxon, or accepted_no on an occurrence row. Provide this or name.

Output parameters:

- `accepted_name` (string): PBDB accepted name (may differ from the searched name).
- `attribution` (string): CC-BY data attribution for the Paleobiology Database.
- `children` (array): One page of immediate child taxa, at most 200 — present only when show_children was true. A taxon with more children than that returns a page, not the full list; read children_truncated before treati…
- `children_offset` (integer): Position in the child list this page started at (0 is the first child). Present only when show_children was true.
- `children_truncated` (boolean): True when more immediate children remain past this page — re-call with children_offset advanced by 200 to read the next. False means this page runs to the end of the child list. Present only when sho…
- `classification` (object): Higher classification of the taxon. Each level is present only when PBDB resolves it.
- `extant` (boolean): True if the clade survives to the present day; false if entirely extinct.
- `first_appearance` (object): A first- or last-appearance window. Empty when PBDB has no dated occurrences.
- `last_appearance` (object): A first- or last-appearance window. Empty when PBDB has no dated occurrences.
- `notice` (string): Guidance when the child list was cut off at the per-page cap (naming the children_offset that reaches the next page), or when children_offset ran past the end of the child list.
- `occurrence_count` (number): Number of fossil occurrences recorded in PBDB, when reported.
- `parent_name` (string): Name of the immediate parent taxon, when known.
- `parent_no` (integer): PBDB taxon id of the immediate parent, when known.
- `rank` (string): Taxonomic rank, e.g. "genus", "family", "order".
- `taxon_no` (integer): Accepted PBDB taxon id — the canonical id for this taxon. Pass it as base_id to paleobiology_search_occurrences, paleobiology_get_diversity, or paleobiology_search_collections to filter on this clade…

### `paleobiology_get_diversity` (~492 tokens)

paleobiology-mcp-server: diversity through time

Compute a diversity / origination / extinction curve for a clade across geologic time, binned by period, epoch, or age — answers "plot dinosaur genus diversity across the Mesozoic." Pass a clade-inclusive base_name (or base_id, the same clade by resolved taxon id — exactly one of the two) and bound the span by a named interval (e.g. "Mesozoic") or a max_ma/min_ma range; choose what to count (genera, species, or families) and the bin resolution. The full bin set returns inline — a diversity series is a bounded set of geologic intervals — so you read the curve, the turnover, and the per-bin origination/extinction directly. Counts reflect SAMPLED diversity, biased by collection effort and rock availability, not true past diversity.

Input parameters:

- `base_id` (integer): Clade-inclusive taxon to count, by PBDB taxon id — the taxon_no from paleobiology_get_taxon, or accepted_no on an occurrence row. Same semantics as base_name, but unambiguous where a name is not (hom…
- `base_name` (string): Clade-inclusive taxon to count, e.g. "Dinosauria" or "Ammonoidea" — this taxon and all descendants. Supply this or base_id (exactly one is required, never both).
- `count` (string): What to count per bin: "genera" (default), "species", or "families".
- `interval` (string): Named geologic interval bounding the span, e.g. "Mesozoic". Alternative to max_ma/min_ma.
- `max_ma` (number): Older bound of the span in millions of years ago. Alternative to interval. When paired with min_ma it must be strictly greater — max_ma is the deeper-time end of the span.
- `min_ma` (number): Younger bound of the span in millions of years ago. Alternative to interval. When paired with max_ma it must be strictly smaller — min_ma is the nearer-to-present end of the span.
- `resolution` (string): Bin resolution: "period" (default, coarse), "epoch", or "age" (finest).

Output parameters:

- `attribution` (string): CC-BY data attribution for the Paleobiology Database.
- `bins` (array): Per-interval diversity bins over the span, ordered oldest-first (oldest geologic interval, highest max_ma, first).
- `notice` (string): Guidance when the clade or span produced no bins, or when the taxon name could not be resolved and was ignored.
- `totalCount` (number): Number of geologic-interval bins returned.

### `paleobiology_list_intervals` (~343 tokens)

paleobiology-mcp-server: list geologic intervals

Look up the geologic time scale — eons, eras, periods, epochs, and ages with their absolute-age boundaries in millions of years (Ma) and nesting. This is the reference that grounds every temporal filter on the other tools and translates a named interval like "Late Cretaceous" to its 100.5–66.0 Ma boundaries (and back). Filter by a name substring, a Ma range (overlap match), and/or a level; call with no filters to browse the full scale. Browsing and every name on the bundled ICS international-scale snapshot are answered offline. A name the snapshot does not carry — the sub-stage and regional names that occurrence and collection rows report, such as "Late Maastrichtian" or "Lancian" — costs one PBDB lookup across its other time scales; the response names which source answered and which scale the interval belongs to.

Input parameters:

- `level` (string): Restrict to one rank of the international scale: eon, era, period, epoch, or age (finest). Browsing is bounded to that scale, so the sub-stage and regional ranks are not selectable here.
- `max_ma` (number): Older bound of an age window (Ma); intervals overlapping [min_ma, max_ma] match.
- `min_ma` (number): Younger bound of an age window (Ma); intervals overlapping [min_ma, max_ma] match.
- `name` (string): Case-insensitive substring of the interval name, e.g. "cretaceous" or "Jurassic". A name the bundled international scale does not carry is matched exactly against PBDB's other time scales.

Output parameters:

- `intervals` (array): Matching geologic intervals, sorted oldest-first.
- `notice` (string): Guidance when no interval matched the filters.
- `snapshot_version` (string): ICS chart version and generation date of the bundled time scale, for citation.
- `source` (string): Which source answered: "bundled_ics" for the offline international-scale snapshot, "pbdb_upstream" for a name resolved live against PBDB's other time scales.
- `totalCount` (number): Number of intervals matched by the filters.

### `paleobiology_search_collections` (~659 tokens)

paleobiology-mcp-server: search fossil collections

Find fossil collections (localities) by area and geologic time — "what has been dug up here, and from what rock." Each locality returns its location, age (named interval and Ma), formation and strata, lithology, depositional environment, and the count of co-occurring fossils. Filter by a clade-inclusive base_name (or base_id, the same clade by resolved taxon id), a named interval or max_ma/min_ma range, a lng/lat bounding box, a formation or lithology name, and/or an environment. Results page inline via limit/offset (the response discloses when more remain). Take a collection_no from a row and pass it — or the same bbox+interval — to paleobiology_search_occurrences to see the actual fauna found together.

Input parameters:

- `base_id` (integer): Clade-inclusive taxon filter by PBDB taxon id — the taxon_no from paleobiology_get_taxon, or accepted_no on an occurrence row. Same semantics as base_name, but unambiguous where a name is not (homony…
- `base_name` (string): Clade-inclusive taxon filter — localities yielding this taxon or its descendants, e.g. "Dinosauria". Supply this or base_id, never both.
- `environment` (string): Depositional environment: "marine", "terrestrial", or "freshwater" (lacustrine + fluvial). Omit for all.
- `formation` (string): Geologic formation name to filter by, e.g. "Hell Creek".
- `interval` (string): Named geologic interval bounding the age, e.g. "Maastrichtian". Alternative to max_ma/min_ma.
- `latmax` (number): Northern edge of the bounding box, decimal degrees (−90…90). Valid on its own — a lone latitude edge filters as a half-plane.
- `latmin` (number): Southern edge of the bounding box, decimal degrees (−90…90). Valid on its own — a lone latitude edge filters as a half-plane.
- `limit` (integer): Maximum localities to return per page (1–500).
- `lithology` (string): Lithology (rock type) to filter by, e.g. "sandstone".
- `lngmax` (number): Eastern edge of the bounding box, decimal degrees (−180…180). Longitude is a closed pair — supply lngmin with it or neither.
- `lngmin` (number): Western edge of the bounding box, decimal degrees (−180…180). Longitude is a closed pair — supply lngmax with it or neither.
- `max_ma` (number): Older age bound in millions of years ago. When paired with min_ma it must be strictly greater — max_ma is the deeper-time end of the window.
- `min_ma` (number): Younger age bound in millions of years ago. When paired with max_ma it must be strictly smaller — min_ma is the nearer-to-present end of the window.
- `offset` (integer): Number of localities to skip — page with limit by advancing offset.

Output parameters:

- `attribution` (string): CC-BY data attribution for the Paleobiology Database.
- `cap` (number): The per-page limit that was applied (set when truncated).
- `collections` (array): Matching localities for this page.
- `notice` (string): Guidance when no locality matched, when localities remain past this page, or when a filter value was not recognized and ignored.
- `shown` (number): Number of localities returned in this page (set when truncated).
- `totalCount` (number): Total localities matching the filters upstream, across all pages.
- `truncated` (boolean): True when localities remain past this page — advance offset for more.

### `paleobiology_dataframe_query` (~224 tokens)

paleobiology-mcp-server: query staged occurrences with SQL

Run a read-only SQL SELECT against occurrence result sets staged on a DataCanvas by paleobiology_search_occurrences. This is how you analyze a large fossil set without re-fetching it: count occurrences by early_interval, group by formation, country (cc), or accepted_name, or filter by a paleo/modern coordinate range. The classification column is JSON — roll up by rank with json_extract_string(classification, '$.family') (also $.phylum, $.class, $.order, $.genus). Staged rows are occurrences, so collection-only fields such as lithology are not present. Reference tables by the table_name that search_occurrences returned — call paleobiology_dataframe_describe first if you do not know the table or column names. SELECT only; writes and file-reading functions are rejected.

Input parameters:

- `canvas_id` (string, required): Canvas id returned by paleobiology_search_occurrences when its result spilled.
- `sql` (string, required): A read-only SQL SELECT. Reference tables by the names paleobiology_search_occurrences / _describe returned.

Output parameters:

- `row_count` (number): Number of rows in the full result before any row cap.
- `rows` (array): Result rows (capped at the canvas row limit). Keys are the selected column names.
- `truncated` (boolean): True when the result exceeded the canvas row cap and rows were trimmed.

### `paleobiology_dataframe_describe` (~75 tokens)

paleobiology-mcp-server: describe staged canvas tables

List the tables and their columns staged on a DataCanvas by paleobiology_search_occurrences. Call this before paleobiology_dataframe_query to discover the exact table_name and column names to reference in SQL.

Input parameters:

- `canvas_id` (string, required): Canvas id returned by paleobiology_search_occurrences when its result spilled.

Output parameters:

- `tables` (array): Tables staged on the canvas.

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/cyanheads-paleobiology-mcp-server/cyanheads-paleobiology-mcp-server#diagnostics

## Score history

- 2026-08-07: 65
- 2026-08-06: 62
- 2026-08-05: 62
- 2026-08-04: 35
- 2026-08-03: 35
- 2026-08-02: 35
- 2026-08-01: 13
- 2026-07-30: 9
- 2026-07-28: 24
- 2026-07-27: 24

## Links

- npm package: https://www.npmjs.com/package/@cyanheads/paleobiology-mcp-server
- Socket report: https://socket.dev/npm/package/@cyanheads/paleobiology-mcp-server
- Repository: https://github.com/cyanheads/paleobiology-mcp-server
- Changelog RSS feed: https://verifymcp.io/servers/cyanheads-paleobiology-mcp-server/cyanheads-paleobiology-mcp-server.xml
- Changelog JSON feed: https://verifymcp.io/servers/cyanheads-paleobiology-mcp-server/cyanheads-paleobiology-mcp-server.json
- HTML version of this page: https://verifymcp.io/servers/cyanheads-paleobiology-mcp-server/cyanheads-paleobiology-mcp-server